From 795f2558579a67ad5c30d39ac9d34f5a5b1b709b Mon Sep 17 00:00:00 2001 From: nilseling Date: Tue, 26 Sep 2023 16:19:56 +0200 Subject: [PATCH 1/4] Updated example data --- inst/extdata/mockData/cpout/Experiment.csv | 4 +- inst/extdata/mockData/cpout/Image.csv | 30 +- .../mockData/cpout/Object_relationships.csv | 1624 ++++++++++------- inst/extdata/mockData/cpout/cell.csv | 448 ++--- inst/extdata/mockData/cpout/panel.csv | 12 +- inst/extdata/mockData/cpout/var_Image.csv | 88 +- inst/extdata/mockData/cpout/var_cell.csv | 168 +- inst/extdata/mockData/steinbock/cells.csv | 219 --- inst/extdata/mockData/steinbock/images.csv | 32 +- .../intensities/20210305_NE_mockData1_001.csv | 18 + .../intensities/20210305_NE_mockData1_002.csv | 22 + .../intensities/20210305_NE_mockData1_003.csv | 26 + .../intensities/20210305_NE_mockData1_1.csv | 9 - .../intensities/20210305_NE_mockData1_2.csv | 13 - .../intensities/20210305_NE_mockData1_3.csv | 13 - .../intensities/20210305_NE_mockData2_001.csv | 56 + .../intensities/20210305_NE_mockData2_002.csv | 22 + .../intensities/20210305_NE_mockData2_003.csv | 31 + .../intensities/20210305_NE_mockData2_1.csv | 13 - .../intensities/20210305_NE_mockData2_2.csv | 12 - .../intensities/20210305_NE_mockData2_3.csv | 13 - .../intensities/20210305_NE_mockData3_001.csv | 21 + .../intensities/20210305_NE_mockData3_002.csv | 27 + .../intensities/20210305_NE_mockData3_003.csv | 23 + .../intensities/20210305_NE_mockData3_1.csv | 14 - .../intensities/20210305_NE_mockData3_2.csv | 13 - .../intensities/20210305_NE_mockData3_3.csv | 10 - .../intensities/20210305_NE_mockData4_001.csv | 10 + .../intensities/20210305_NE_mockData4_002.csv | 27 + .../intensities/20210305_NE_mockData4_003.csv | 35 + .../intensities/20210305_NE_mockData4_1.csv | 8 - .../intensities/20210305_NE_mockData4_2.csv | 15 - .../intensities/20210305_NE_mockData4_3.csv | 25 - .../intensities/20210305_NE_mockData5_001.csv | 17 + .../intensities/20210305_NE_mockData5_002.csv | 43 + .../intensities/20210305_NE_mockData5_003.csv | 41 + .../intensities/20210305_NE_mockData5_1.csv | 13 - .../intensities/20210305_NE_mockData5_2.csv | 31 - .../intensities/20210305_NE_mockData5_3.csv | 31 - .../neighbors/20210305_NE_mockData1_001.csv | 51 + .../neighbors/20210305_NE_mockData1_002.csv | 79 + .../neighbors/20210305_NE_mockData1_003.csv | 103 ++ .../neighbors/20210305_NE_mockData1_1.csv | 23 - .../neighbors/20210305_NE_mockData1_2.csv | 47 - .../neighbors/20210305_NE_mockData1_3.csv | 49 - .../neighbors/20210305_NE_mockData2_001.csv | 257 +++ .../neighbors/20210305_NE_mockData2_002.csv | 61 + .../neighbors/20210305_NE_mockData2_003.csv | 129 ++ .../neighbors/20210305_NE_mockData2_1.csv | 42 - .../neighbors/20210305_NE_mockData2_2.csv | 31 - .../neighbors/20210305_NE_mockData2_3.csv | 50 - .../neighbors/20210305_NE_mockData3_001.csv | 81 + .../neighbors/20210305_NE_mockData3_002.csv | 105 ++ .../neighbors/20210305_NE_mockData3_003.csv | 79 + .../neighbors/20210305_NE_mockData3_1.csv | 52 - .../neighbors/20210305_NE_mockData3_2.csv | 50 - .../neighbors/20210305_NE_mockData3_3.csv | 27 - .../neighbors/20210305_NE_mockData4_001.csv | 37 + .../neighbors/20210305_NE_mockData4_002.csv | 121 ++ .../neighbors/20210305_NE_mockData4_003.csv | 141 ++ .../neighbors/20210305_NE_mockData4_1.csv | 27 - .../neighbors/20210305_NE_mockData4_2.csv | 71 - .../neighbors/20210305_NE_mockData4_3.csv | 114 -- .../neighbors/20210305_NE_mockData5_001.csv | 69 + .../neighbors/20210305_NE_mockData5_002.csv | 201 ++ .../neighbors/20210305_NE_mockData5_003.csv | 175 ++ .../neighbors/20210305_NE_mockData5_1.csv | 61 - .../neighbors/20210305_NE_mockData5_2.csv | 164 -- .../neighbors/20210305_NE_mockData5_3.csv | 157 -- inst/extdata/mockData/steinbock/panel.csv | 12 +- .../regionprops/20210305_NE_mockData1_001.csv | 18 + .../regionprops/20210305_NE_mockData1_002.csv | 22 + .../regionprops/20210305_NE_mockData1_003.csv | 26 + .../regionprops/20210305_NE_mockData1_1.csv | 9 - .../regionprops/20210305_NE_mockData1_2.csv | 13 - .../regionprops/20210305_NE_mockData1_3.csv | 13 - .../regionprops/20210305_NE_mockData2_001.csv | 56 + .../regionprops/20210305_NE_mockData2_002.csv | 22 + .../regionprops/20210305_NE_mockData2_003.csv | 31 + .../regionprops/20210305_NE_mockData2_1.csv | 13 - .../regionprops/20210305_NE_mockData2_2.csv | 12 - .../regionprops/20210305_NE_mockData2_3.csv | 13 - .../regionprops/20210305_NE_mockData3_001.csv | 21 + .../regionprops/20210305_NE_mockData3_002.csv | 27 + .../regionprops/20210305_NE_mockData3_003.csv | 23 + .../regionprops/20210305_NE_mockData3_1.csv | 14 - .../regionprops/20210305_NE_mockData3_2.csv | 13 - .../regionprops/20210305_NE_mockData3_3.csv | 10 - .../regionprops/20210305_NE_mockData4_001.csv | 10 + .../regionprops/20210305_NE_mockData4_002.csv | 27 + .../regionprops/20210305_NE_mockData4_003.csv | 35 + .../regionprops/20210305_NE_mockData4_1.csv | 8 - .../regionprops/20210305_NE_mockData4_2.csv | 15 - .../regionprops/20210305_NE_mockData4_3.csv | 25 - .../regionprops/20210305_NE_mockData5_001.csv | 17 + .../regionprops/20210305_NE_mockData5_002.csv | 43 + .../regionprops/20210305_NE_mockData5_003.csv | 41 + .../regionprops/20210305_NE_mockData5_1.csv | 13 - .../regionprops/20210305_NE_mockData5_2.csv | 31 - .../regionprops/20210305_NE_mockData5_3.csv | 31 - inst/extdata/mockData/steinbock/steinbock.sh | 28 +- inst/scripts/download_TestData_cpout.Rmd | 2 +- inst/scripts/download_TestData_steinbock.Rmd | 6 +- 103 files changed, 3903 insertions(+), 2728 deletions(-) delete mode 100644 inst/extdata/mockData/steinbock/cells.csv create mode 100644 inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_001.csv create mode 100644 inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_002.csv create mode 100644 inst/extdata/mockData/steinbock/intensities/20210305_NE_mockData1_003.csv delete mode 100644 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100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_3.csv create mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv create mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_002.csv create mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv delete mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_1.csv delete mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_2.csv delete mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_3.csv create mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv create mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv create mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv delete mode 100644 inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_1.csv delete mode 100644 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create mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_002.csv create mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_003.csv delete mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_1.csv delete mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_2.csv delete mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData4_3.csv create mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_001.csv create mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_002.csv create mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_003.csv delete mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_1.csv delete mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_2.csv delete mode 100644 inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_3.csv diff --git a/inst/extdata/mockData/cpout/Experiment.csv b/inst/extdata/mockData/cpout/Experiment.csv index faffcfa..c57252b 100644 --- a/inst/extdata/mockData/cpout/Experiment.csv +++ b/inst/extdata/mockData/cpout/Experiment.csv @@ -3,7 +3,7 @@ CellProfiler_Version,4.2.1 ChannelType_FullStack,Color ChannelType_ProbabStack,Color ChannelType_cellmask,Grayscale -ImageSet_Zip_Dictionary,b'PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz48T01FIHhtbG5zPSJodHRwOi8vd3d3Lm9wZW5taWNyb3Njb3B5Lm9yZy9TY2hlbWFzL09NRS8yMDE2LTA2Ij48SW1hZ2UgSUQ9IkZ1bGxTdGFjayI+PFBpeGVscyBEaW1lbnNpb25PcmRlcj0iWFlDWlQiIElEPSJQaXhlbHM6RnVsbFN0YWNrIiBTaXplQz0iMSIgU2l6ZVQ9IjEiIFNpemVYPSIxIiBTaXplWT0iMSI+PFRpZmZEYXRhIEZpcnN0Qz0iMCIgRmlyc3RUPSIwIiBGaXJzdFo9IjAiIElGRD0iMCIgUGxhbmVDb3VudD0iMSI+PFVVSUQgRmlsZU5hbWU9ImZpbGU6L1VzZXJzL25pbHMvR2l0aHViL1Rlc3REYXRhL2RhdGFzZXRzLzIxMDMwOF9JbWNUZXN0RGF0YS9hbmFseXNpcy9jcG91dC9pbWFnZXMvMjAyMTAzMDVfTkVfbW9ja0RhdGExX3MwX2ExX2FjX2Z1bGwudGlmZiIvPjwvVGlmZkRhdGE+PFBsYW5lIFRoZUM9IjAiIFRoZVQ9IjAiIFRoZVo9IjAiPjxBbm5vdGF0aW9uUmVmIElEPSJpbmZvOi8vY2VsbHByb2ZpbGVyLm9yZy9pbWFnZXNldC9hbm5vdGF0aW9uLzIwMTQtMDQtMTcvQ2hhbm5lbC8tMiIvPjwvUGxhbmU+PC9QaXhlbHM+PC9JbWFnZT48SW1hZ2UgSUQ9IlByb2JhYlN0YWNrIj48UGl4ZWxzIERpbWVuc2lvbk9yZGVyPSJYWUNaVCIgSUQ9IlBpeGVsczpQcm9iYWJTdGFjayIgU2l6ZUM9IjEiIFNpemVUPSIxIiBTaXplWD0iMSIgU2l6ZVk9IjEiPjxUaWZmRGF0YSBGaXJzdEM9IjAiIEZpcnN0VD0iMCIgRmlyc3RaPSIwIiBJRkQ9IjAiIFBsYW5lQ291bnQ9IjEiPjxVVUlEIEZpbGVOYW1lPSJmaWxlOi9Vc2Vycy9uaWxzL0dpdGh1Yi9UZXN0RGF0YS9kYXRhc2V0cy8yMTAzMDhfSW1jVGVzdERhdGEvYW5hbHlzaXMvY3BvdXQvcHJvYmFiaWxpdGllcy8yMDIxMDMwNV9ORV9tb2NrRGF0YV9zMF9hMV9hY19pbGFzdGlrX3MyX1Byb2JhYmlsaXRpZXNfczEudGlmZiIvPjwvVGlmZkRhdGE+PFBsYW5lIFRoZUM9IjAiIFRoZVQ9IjAiIFRoZVo9IjAiPjxBbm5vdGF0aW9uUmVmIElEPSJpbmZvOi8vY2VsbHByb2ZpbGVyLm9yZy9pbWFnZXNldC9hbm5vdGF0aW9uLzIwMTQtMDQtMTcvQ2hhbm5lbC8tMiIvPjwvUGxhbmU+PC9QaXhlbHM+PC9JbWFnZT48SW1hZ2UgSUQ9ImNlbGxtYXNrIj48UGl4ZWxzIERpbWVuc2lvbk9yZGVyPSJYWUNaVCIgSUQ9IlBpeGVsczpjZWxsbWFzayIgU2l6ZVQ9IjEiIFNpemVYPSIxIiBTaXplWT0iMSI+PFRpZmZEYXRhIEZpcnN0Qz0iMCIgRmlyc3RUPSIwIiBGaXJzdFo9IjAiIElGRD0iMCIgUGxhbmVDb3VudD0iMSI+PFVVSUQgRmlsZU5hbWU9ImZpbGU6L1VzZXJzL25pbHMvR2l0aHViL1Rlc3REYXRhL2RhdGFzZXRzLzIxMDMwOF9JbWNUZXN0RGF0YS9hbmFseXNpcy9jcG91dC9tYXNrcy8yMDIxMDMwNV9ORV9tb2NrRGF0YTFfczBfYTFfYWNfaWxhc3Rpa19zMl9Qcm9iYWJpbGl0aWVzXz48L1B4cz48L0ltZExvbmdBbm5vdGF0aW9uY3JoYW5uRGVzY3JpcHRpb24+VmFsdWU+PGFsdGlvbj48U3RydWN0dXJlZEFubm90YXRpb25zPjxPZXMvMjAyMTAzMDVfTkVfbW9ja0RhdGEyX3MwX2ExX2FjX3MvMjAyMTAzMDVfTkVfbW9ja0RhdGEyX3MwX2ExX2FjX2lsYXN0aWtfczJfUHJvYmFiaWxpdGllc19lcy8yMDIxMDMwNV9ORV9tb2NrRGF0YTNfczBfYTFfYWNfcy8yMDIxMDMwNV9ORV9tb2NrRGF0YTNfczBfYTFfYWNfaWxhc3Rpa19zMl9Qcm9iYWJpbGl0aWVzX2VzLzIwMjEwMzA1X05FX21vY2tEYXRhNF9zMF9hMV9hY19zLzIwMjEwMzA1X05FX21vY2tEYXRhNF9zMF9hMV9hY19pbGFzdGlrX3MyX1Byb2JhYmlsaXRpZXNfeG1sc2lvbjEuMCJlbmNvbmdGOD9PTUVuc3A6L3d3Lm9waXNjeS5vcmcvU21hcy9PTUUvMjAtNj48SW1hZ2UgSUQ9IlN0YWNrIj48UGl4ZWxzIERpbWVuc2lvbk9yZGVyPSJYWUNaVCIgSUQ9IlBpeGVsczpGdWxsU3RhY2siIFNpemVDPSIxIiBTaXplVD0iMSIgU2l6ZVg9IjEiIFNpemVZPSIxIj48VGlmZkRhdGEgRmlyc3RDPSIwIiBGaXJzdFQ9IjAiIEZpcnN0Wj0iMCIgSUZEPSIwIiBQbGFuZUNvdW50PSIxIj48VVVJRCBGaWxlTmFtZT0iZmlsZTovVXNlcnMvbmlscy9HaXRodWIvVGVzdERhdGEvZGF0YXNldHMvMjEwMzA4X0ltY1Rlc3REYXRhL2FuYWx5c2lzL2Nwb3V0L2ltYWdlcy8yMDIxMDMwNV9ORV9tb2NrRGF0YTVfczBfYTFfYWNfdWxsLnRpZmYiLz48L1RpZmZEYXRhPjxQbGFuZSBUaGVDPSIwIiBUaGVUPSIwIiBUaGVaPSIwIj48QW5ub3RhdGlvblJlZiBJRD0iaW5mbzovL2NlbGxwcm9maWxlci5vcmcvaW1hZ2VzZXQvYW5ub3RhdGlvbi8yMDE0LTA0LTE3L0NoYW5uZWwvLTIiLz48L1BsYW5lPjwvUGl4ZWxzPjwvSW1hZ2U+PEltYWdlIElEPSJQcm9iYWJTdGNrUHJvYmFiU3RhY2siIFNpemVDPSIxIiBTaXplWD0iMSJZPSIxIj48VGlmZkRhdGEgRmlyc3RDPSIwIiBGaXJzdFQ9IjAiIFo9IjAiRD0ibGFvdT0iMVVJRCBGaU5hbWU9ImZpbGU6c2Vyc2l0dWIvVGF0cy8zX2NUZXN0RGF0YS9hbnRwcm9iYWJpbGl0aWVzLzIyMTAzMDVfTl9zX2ExX2FjaWwyX3JvdGlpZmY+PFBsYW5lIFRoZUM9IjAiIFRoZVQ9IjAiWj0iMCI+PEFubm90YXRpb25mIElpbm86Ly9jZXJnaW1hc2V0L25ub3RhdGlvbi8yMDE0LTA0Q2hhbm5lbC8tMiIvPjwvZT48L1BpeGVscz48L0ltYWdlPjxJbWFnZSBjZWxsbWFzaz48UGl4ZWxzIHNpVCIgSUQ9IlBjZWxsbWFzayJtcy8yMDIxMDMwNV9ORV9tb2NrRGF0YTVfczBfYTFfYWNfaWxhc3Rpa19zMl9Qcm9iYWJpbGl0aWVzXw==' +ImageSet_Zip_Dictionary,b'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' Metadata_Tags,"[""Metadata_acname"", ""Metadata_acid""]" Pipeline_Pipeline,"CellProfiler Pipeline: http://www.cellprofiler.org Version:5 @@ -204,4 +204,4 @@ CreateBatchFiles:[module_num:15|svn_version:'Unknown'|variable_revision_number:8 Local root path:/home/vitoz Cluster root path:/home/vitoz " -Run_Timestamp,2022-04-03T15:18:45.272649 +Run_Timestamp,2023-09-26T13:38:38.234878 diff --git a/inst/extdata/mockData/cpout/Image.csv b/inst/extdata/mockData/cpout/Image.csv index c35fed7..d3a161d 100644 --- a/inst/extdata/mockData/cpout/Image.csv +++ b/inst/extdata/mockData/cpout/Image.csv @@ -1,16 +1,16 @@ Channel_FullStack,Channel_ProbabStack,Channel_cellmask,Count_cell,ExecutionTime_01Images,ExecutionTime_02Metadata,ExecutionTime_03NamesAndTypes,ExecutionTime_04Groups,ExecutionTime_05ConvertImageToObjects,ExecutionTime_06MeasureObjectNeighbors,ExecutionTime_07MeasureObjectIntensityMultichannel,ExecutionTime_08MeasureObjectIntensityMultichannel,ExecutionTime_09MeasureObjectSizeShape,ExecutionTime_10MeasureImageIntensityMultichannel,ExecutionTime_11MeasureImageIntensityMultichannel,FileName_FullStack,FileName_ProbabStack,FileName_cellmask,Frame_FullStack,Frame_ProbabStack,Frame_cellmask,Group_Index,Group_Number,Height_FullStack,Height_ProbabStack,Height_cellmask,ImageNumber,ImageSet_ImageSet,Intensity_LowerQuartileIntensity_FullStack_c1,Intensity_LowerQuartileIntensity_FullStack_c2,Intensity_LowerQuartileIntensity_FullStack_c3,Intensity_LowerQuartileIntensity_FullStack_c4,Intensity_LowerQuartileIntensity_FullStack_c5,Intensity_LowerQuartileIntensity_ProbabStack_c1,Intensity_LowerQuartileIntensity_ProbabStack_c2,Intensity_LowerQuartileIntensity_ProbabStack_c3,Intensity_MADIntensity_FullStack_c1,Intensity_MADIntensity_FullStack_c2,Intensity_MADIntensity_FullStack_c3,Intensity_MADIntensity_FullStack_c4,Intensity_MADIntensity_FullStack_c5,Intensity_MADIntensity_ProbabStack_c1,Intensity_MADIntensity_ProbabStack_c2,Intensity_MADIntensity_ProbabStack_c3,Intensity_MaxIntensity_FullStack_c1,Intensity_MaxIntensity_FullStack_c2,Intensity_MaxIntensity_FullStack_c3,Intensity_MaxIntensity_FullStack_c4,Intensity_MaxIntensity_FullStack_c5,Intensity_MaxIntensity_ProbabStack_c1,Intensity_MaxIntensity_ProbabStack_c2,Intensity_MaxIntensity_ProbabStack_c3,Intensity_MeanIntensity_FullStack_c1,Intensity_MeanIntensity_FullStack_c2,Intensity_MeanIntensity_FullStack_c3,Intensity_MeanIntensity_FullStack_c4,Intensity_MeanIntensity_FullStack_c5,Intensity_MeanIntensity_ProbabStack_c1,Intensity_MeanIntensity_ProbabStack_c2,Intensity_MeanIntensity_ProbabStack_c3,Intensity_MedianIntensity_FullStack_c1,Intensity_MedianIntensity_FullStack_c2,Intensity_MedianIntensity_FullStack_c3,Intensity_MedianIntensity_FullStack_c4,Intensity_MedianIntensity_FullStack_c5,Intensity_MedianIntensity_ProbabStack_c1,Intensity_MedianIntensity_ProbabStack_c2,Intensity_MedianIntensity_ProbabStack_c3,Intensity_MinIntensity_FullStack_c1,Intensity_MinIntensity_FullStack_c2,Intensity_MinIntensity_FullStack_c3,Intensity_MinIntensity_FullStack_c4,Intensity_MinIntensity_FullStack_c5,Intensity_MinIntensity_ProbabStack_c1,Intensity_MinIntensity_ProbabStack_c2,Intensity_MinIntensity_ProbabStack_c3,Intensity_PercentMaximal_FullStack_c1,Intensity_PercentMaximal_FullStack_c2,Intensity_PercentMaximal_FullStack_c3,Intensity_PercentMaximal_FullStack_c4,Intensity_PercentMaximal_FullStack_c5,Intensity_PercentMaximal_ProbabStack_c1,Intensity_PercentMaximal_ProbabStack_c2,Intensity_PercentMaximal_ProbabStack_c3,Intensity_StdIntensity_FullStack_c1,Intensity_StdIntensity_FullStack_c2,Intensity_StdIntensity_FullStack_c3,Intensity_StdIntensity_FullStack_c4,Intensity_StdIntensity_FullStack_c5,Intensity_StdIntensity_ProbabStack_c1,Intensity_StdIntensity_ProbabStack_c2,Intensity_StdIntensity_ProbabStack_c3,Intensity_TotalArea_FullStack_c1,Intensity_TotalArea_FullStack_c2,Intensity_TotalArea_FullStack_c3,Intensity_TotalArea_FullStack_c4,Intensity_TotalArea_FullStack_c5,Intensity_TotalArea_ProbabStack_c1,Intensity_TotalArea_ProbabStack_c2,Intensity_TotalArea_ProbabStack_c3,Intensity_TotalIntensity_FullStack_c1,Intensity_TotalIntensity_FullStack_c2,Intensity_TotalIntensity_FullStack_c3,Intensity_TotalIntensity_FullStack_c4,Intensity_TotalIntensity_FullStack_c5,Intensity_TotalIntensity_ProbabStack_c1,Intensity_TotalIntensity_ProbabStack_c2,Intensity_TotalIntensity_ProbabStack_c3,Intensity_UpperQuartileIntensity_FullStack_c1,Intensity_UpperQuartileIntensity_FullStack_c2,Intensity_UpperQuartileIntensity_FullStack_c3,Intensity_UpperQuartileIntensity_FullStack_c4,Intensity_UpperQuartileIntensity_FullStack_c5,Intensity_UpperQuartileIntensity_ProbabStack_c1,Intensity_UpperQuartileIntensity_ProbabStack_c2,Intensity_UpperQuartileIntensity_ProbabStack_c3,MD5Digest_FullStack,MD5Digest_ProbabStack,MD5Digest_cellmask,Metadata_,Metadata_FileLocation,Metadata_Frame,Metadata_Series,Metadata_ablation_distance_between_shots_x,Metadata_ablation_distance_between_shots_y,Metadata_ablation_frequency,Metadata_ablation_power,Metadata_acid,Metadata_acname,Metadata_description,Metadata_end_timestamp,Metadata_has_after_ablation_image,Metadata_has_before_ablation_image,Metadata_is_valid,Metadata_max_x,Metadata_max_y,Metadata_movement_type,Metadata_origin,Metadata_profiling_type,Metadata_roi_end_x_pos_um,Metadata_roi_end_y_pos_um,Metadata_roi_start_x_pos_um,Metadata_roi_start_y_pos_um,Metadata_segment_data_format,Metadata_signal_type,Metadata_slide_id,Metadata_slideid,Metadata_source_path,Metadata_start_timestamp,Metadata_template,ModuleError_01Images,ModuleError_02Metadata,ModuleError_03NamesAndTypes,ModuleError_04Groups,ModuleError_05ConvertImageToObjects,ModuleError_06MeasureObjectNeighbors,ModuleError_07MeasureObjectIntensityMultichannel,ModuleError_08MeasureObjectIntensityMultichannel,ModuleError_09MeasureObjectSizeShape,ModuleError_10MeasureImageIntensityMultichannel,ModuleError_11MeasureImageIntensityMultichannel,PathName_FullStack,PathName_ProbabStack,PathName_cellmask,ProcessingStatus,Scaling_FullStack,Scaling_ProbabStack,Scaling_cellmask,Series_FullStack,Series_ProbabStack,Series_cellmask,URL_FullStack,URL_ProbabStack,URL_cellmask,Width_FullStack,Width_ProbabStack,Width_cellmask --2,-2,-1,4.0,0.0,0.0,1.230000000000004,0.0,0.01999999999999602,0.05999999999998806,0.37000000000000455,0.1599999999999966,0.04000000000000625,0.04000000000000625,0.020000000000010232,20210305_NE_mockData1_s0_a1_ac_full.tiff,20210305_NE_mockData1_s0_a1_ac_ilastik_s2_Probabilities_s1.tiff,20210305_NE_mockData1_s0_a1_ac_ilastik_s2_Probabilities_mask.tiff,0,0,0,1,1,60,60,60,1,b'eLuj8Hzisxltmw6uzD3aNh0mcUy4bUpMk2W0cTp0YpyyxilINzlxrY8lNnC0VlHbvFRKFQqggCwuSExOJdc0YKwgt7yhZtvoIwvaQNrjukY2+tCWuT6qb4ACOHwNqovsAN+qRxg=',0.0,0.0,0.0,0.0,0.0,0.00999466,0.00999466,0.9699855,0.0,0.0,0.0,0.0,0.0,0.0,0.0,3.0517578e-05,3.0518044e-05,0.00010681315,4.5777066e-05,4.5777066e-05,7.629511e-05,0.065308616,0.2095369,0.9981842,4.1962310206145046e-07,3.5138135879404014e-06,5.764519381854269e-07,4.662478911793894e-07,1.0766087669051356e-06,0.01035037146674262,0.017884123060438368,0.9717484537760417,0.0,0.0,0.0,0.0,0.0,0.00999466,0.00999466,0.9799954,0.0,0.0,0.0,0.0,0.0,0.0,0.0010376135,0.7468223,0.1111111111111111,0.027777777777777776,0.027777777777777776,0.027777777777777776,0.027777777777777776,0.027777777777777776,0.027777777777777776,0.027777777777777776,2.5969928e-06,9.66438e-06,3.0609276e-06,2.7466106e-06,4.606431e-06,0.0036315992,0.017763887,0.020139309,3600,3600,3600,3600,3600,3600,3600,3600,0.0015106432,0.012649729,0.002075227,0.0016784924,0.0038757916,37.261337,64.38284,3498.2944,0.0,0.0,0.0,0.0,0.0,0.00999466,0.019958802,0.9799954,a58b7ef081194a70f42086ea18f2fd94,b0ec30b533d8cc0b452bdcbb641351fa,d795879497baf8e5c52fadb3c5c9116b,0,nan,0,0,1.0,1.0,200.0,5.0,1,20210305_NE_mockData1,ROI_001,2021-03-05T13:36:53.2377649+01:00,False,False,True,60,60,XRaster,mcd,Local,31140.501,13390.28,31080000.0,13449000.0,Float,Dual,0,0,/Users/nils/Github/ImcSegmentationPipeline/scripts/../../TestData/datasets/210308_ImcTestData/raw/20210305_NE_mockData1/20210305_NE_mockData1.mcd,2021-03-05T13:36:08.3473821+01:00,mock_panel,0,0,0,0,0,0,0,0,0,0,0,/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/images,/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/probabilities,/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/masks,Done,65535,65535,65535,0,0,0,file:/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/images/20210305_NE_mockData1_s0_a1_ac_full.tiff,file:/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/probabilities/20210305_NE_mockData1_s0_a1_ac_ilastik_s2_Probabilities_s1.tiff,file:/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/masks/20210305_NE_mockData1_s0_a1_ac_ilastik_s2_Probabilities_mask.tiff,60,60,60 --2,-2,-1,12.0,0.0,0.0,1.8699999999999903,0.0,0.04999999999999716,0.09000000000000341,0.5600000000000023,0.21000000000000796,0.060000000000002274,0.04999999999999716,0.030000000000001137,20210305_NE_mockData1_s0_a2_ac_full.tiff,20210305_NE_mockData1_s0_a2_ac_ilastik_s2_Probabilities_s1.tiff,20210305_NE_mockData1_s0_a2_ac_ilastik_s2_Probabilities_mask.tiff,0,0,0,2,1,51,51,51,2,b'eLuj8Hzisxltmw6uzA2px4xG26ZDPY4Jt02Ronq0cToCGqf4Yxqkm5y41scSGzhaq6htXiqlCgVQQBYXJCankmsaMFaQW95Qs230kQVtIO1xXSMbfWjLXB/VN0ABHL4G1UV2AOndRxs=',0.0,0.0,0.0,0.0,0.0,0.0,0.0072022583,0.0032654307,0.0,0.0,0.0,0.0,4.5777066e-05,0.002761883,0.4120241,0.31119248,0.0010070954,0.00047302968,0.0022430762,0.00080872816,0.0011291676,0.99993896,1.0,1.0,7.863258075553413e-06,2.343550224003254e-05,9.240496757568097e-05,3.692739204887082e-05,0.00011885113210654726,0.07068210489609662,0.4836122849408318,0.4456943437164905,0.0,0.0,0.0,0.0,4.5777066e-05,0.002761883,0.5577325,0.31119248,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.030637254901960783,0.030637254901960783,0.030637254901960783,0.030637254901960783,0.030637254901960783,0.030637254901960783,0.21446078431372548,17.800245098039216,3.999633e-05,5.1040606e-05,0.00023271325,6.49943e-05,0.00016412004,0.2027811,0.40435252,0.42794392,3264,3264,3264,3264,3264,3264,3264,3264,0.025665674,0.07649348,0.3016098,0.12053101,0.3879301,230.70639,1578.5105,1454.7463,0.0,1.5259022e-05,4.5777066e-05,4.5777066e-05,0.00018310826,0.022995345,0.9094377,0.98999006,eaa1b199f9ef9d986c5efa75ef164179,60d22153950c860b10dcf0faeb8def0b,40d74570518dc2d9c485a078fca6bc64,1,nan,0,0,1.0,1.0,200.0,5.0,2,20210305_NE_mockData1,ROI_002,2021-03-05T13:37:44.1120873+01:00,False,False,True,64,51,XRaster,mcd,Local,31948.494,14078.232,31884000.0,14128000.0,Float,Dual,0,0,/Users/nils/Github/ImcSegmentationPipeline/scripts/../../TestData/datasets/210308_ImcTestData/raw/20210305_NE_mockData1/20210305_NE_mockData1.mcd,2021-03-05T13:37:02.3618398+01:00,mock_panel,0,0,0,0,0,0,0,0,0,0,0,/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/images,/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/probabilities,/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/masks,Done,65535,65535,65535,0,0,0,file:/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/images/20210305_NE_mockData1_s0_a2_ac_full.tiff,file:/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/probabilities/20210305_NE_mockData1_s0_a2_ac_ilastik_s2_Probabilities_s1.tiff,file:/Users/nils/Github/TestData/datasets/210308_ImcTestData/analysis/cpout/masks/20210305_NE_mockData1_s0_a2_ac_ilastik_s2_Probabilities_mask.tiff,64,64,64 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diff --git a/inst/extdata/mockData/cpout/Object_relationships.csv b/inst/extdata/mockData/cpout/Object_relationships.csv index 759814c..165acdb 100644 --- a/inst/extdata/mockData/cpout/Object_relationships.csv +++ b/inst/extdata/mockData/cpout/Object_relationships.csv @@ -1,47 +1,63 @@ Module,Module Number,Relationship,First Object Name,First Image Number,First Object Number,Second Object Name,Second Image Number,Second Object Number -MeasureObjectNeighbors,6,Neighbors,cell,1,2,cell,1,3 -MeasureObjectNeighbors,6,Neighbors,cell,1,3,cell,1,2 -MeasureObjectNeighbors,6,Neighbors,cell,1,3,cell,1,4 -MeasureObjectNeighbors,6,Neighbors,cell,1,4,cell,1,3 +MeasureObjectNeighbors,6,Neighbors,cell,1,1,cell,1,2 +MeasureObjectNeighbors,6,Neighbors,cell,1,1,cell,1,4 +MeasureObjectNeighbors,6,Neighbors,cell,1,2,cell,1,1 +MeasureObjectNeighbors,6,Neighbors,cell,1,2,cell,1,4 +MeasureObjectNeighbors,6,Neighbors,cell,1,3,cell,1,5 +MeasureObjectNeighbors,6,Neighbors,cell,1,4,cell,1,1 +MeasureObjectNeighbors,6,Neighbors,cell,1,4,cell,1,2 +MeasureObjectNeighbors,6,Neighbors,cell,1,5,cell,1,3 +MeasureObjectNeighbors,6,Neighbors,cell,1,5,cell,1,6 +MeasureObjectNeighbors,6,Neighbors,cell,1,5,cell,1,7 +MeasureObjectNeighbors,6,Neighbors,cell,1,6,cell,1,5 +MeasureObjectNeighbors,6,Neighbors,cell,1,6,cell,1,7 +MeasureObjectNeighbors,6,Neighbors,cell,1,7,cell,1,5 +MeasureObjectNeighbors,6,Neighbors,cell,1,7,cell,1,6 +MeasureObjectNeighbors,6,Neighbors,cell,1,7,cell,1,8 +MeasureObjectNeighbors,6,Neighbors,cell,1,7,cell,1,9 +MeasureObjectNeighbors,6,Neighbors,cell,1,8,cell,1,7 +MeasureObjectNeighbors,6,Neighbors,cell,1,8,cell,1,9 +MeasureObjectNeighbors,6,Neighbors,cell,1,9,cell,1,7 +MeasureObjectNeighbors,6,Neighbors,cell,1,9,cell,1,8 MeasureObjectNeighbors,6,Neighbors,cell,5,1,cell,5,2 MeasureObjectNeighbors,6,Neighbors,cell,5,1,cell,5,4 -MeasureObjectNeighbors,6,Neighbors,cell,5,1,cell,5,6 MeasureObjectNeighbors,6,Neighbors,cell,5,2,cell,5,1 MeasureObjectNeighbors,6,Neighbors,cell,5,2,cell,5,3 MeasureObjectNeighbors,6,Neighbors,cell,5,2,cell,5,4 +MeasureObjectNeighbors,6,Neighbors,cell,5,2,cell,5,5 MeasureObjectNeighbors,6,Neighbors,cell,5,3,cell,5,2 MeasureObjectNeighbors,6,Neighbors,cell,5,3,cell,5,4 MeasureObjectNeighbors,6,Neighbors,cell,5,3,cell,5,5 MeasureObjectNeighbors,6,Neighbors,cell,5,3,cell,5,7 +MeasureObjectNeighbors,6,Neighbors,cell,5,3,cell,5,8 MeasureObjectNeighbors,6,Neighbors,cell,5,3,cell,5,9 MeasureObjectNeighbors,6,Neighbors,cell,5,4,cell,5,1 MeasureObjectNeighbors,6,Neighbors,cell,5,4,cell,5,2 MeasureObjectNeighbors,6,Neighbors,cell,5,4,cell,5,3 -MeasureObjectNeighbors,6,Neighbors,cell,5,4,cell,5,5 MeasureObjectNeighbors,6,Neighbors,cell,5,4,cell,5,8 +MeasureObjectNeighbors,6,Neighbors,cell,5,5,cell,5,2 MeasureObjectNeighbors,6,Neighbors,cell,5,5,cell,5,3 -MeasureObjectNeighbors,6,Neighbors,cell,5,5,cell,5,4 MeasureObjectNeighbors,6,Neighbors,cell,5,5,cell,5,7 MeasureObjectNeighbors,6,Neighbors,cell,5,5,cell,5,9 -MeasureObjectNeighbors,6,Neighbors,cell,5,6,cell,5,1 MeasureObjectNeighbors,6,Neighbors,cell,5,6,cell,5,8 MeasureObjectNeighbors,6,Neighbors,cell,5,6,cell,5,10 MeasureObjectNeighbors,6,Neighbors,cell,5,7,cell,5,3 MeasureObjectNeighbors,6,Neighbors,cell,5,7,cell,5,5 MeasureObjectNeighbors,6,Neighbors,cell,5,7,cell,5,9 +MeasureObjectNeighbors,6,Neighbors,cell,5,8,cell,5,3 MeasureObjectNeighbors,6,Neighbors,cell,5,8,cell,5,4 MeasureObjectNeighbors,6,Neighbors,cell,5,8,cell,5,6 +MeasureObjectNeighbors,6,Neighbors,cell,5,8,cell,5,9 MeasureObjectNeighbors,6,Neighbors,cell,5,8,cell,5,10 MeasureObjectNeighbors,6,Neighbors,cell,5,8,cell,5,11 MeasureObjectNeighbors,6,Neighbors,cell,5,9,cell,5,3 MeasureObjectNeighbors,6,Neighbors,cell,5,9,cell,5,5 MeasureObjectNeighbors,6,Neighbors,cell,5,9,cell,5,7 -MeasureObjectNeighbors,6,Neighbors,cell,5,9,cell,5,11 +MeasureObjectNeighbors,6,Neighbors,cell,5,9,cell,5,8 MeasureObjectNeighbors,6,Neighbors,cell,5,10,cell,5,6 MeasureObjectNeighbors,6,Neighbors,cell,5,10,cell,5,8 MeasureObjectNeighbors,6,Neighbors,cell,5,10,cell,5,11 MeasureObjectNeighbors,6,Neighbors,cell,5,11,cell,5,8 -MeasureObjectNeighbors,6,Neighbors,cell,5,11,cell,5,9 MeasureObjectNeighbors,6,Neighbors,cell,5,11,cell,5,10 MeasureObjectNeighbors,6,Neighbors,cell,3,1,cell,3,2 MeasureObjectNeighbors,6,Neighbors,cell,3,1,cell,3,3 @@ -51,336 +67,398 @@ MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,1 MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,3 MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,4 MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,5 -MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,7 -MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,8 -MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,10 +MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,6 +MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,9 +MeasureObjectNeighbors,6,Neighbors,cell,3,2,cell,3,11 MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,1 MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,2 MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,4 MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,5 MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,7 -MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,8 +MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,9 +MeasureObjectNeighbors,6,Neighbors,cell,3,3,cell,3,11 MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,1 MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,2 MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,3 +MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,5 MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,6 -MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,7 MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,8 -MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,10 +MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,9 +MeasureObjectNeighbors,6,Neighbors,cell,3,4,cell,3,11 MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,2 MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,3 +MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,4 MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,7 -MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,8 MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,9 -MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,10 +MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,11 +MeasureObjectNeighbors,6,Neighbors,cell,3,5,cell,3,12 MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,1 +MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,2 MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,4 -MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,7 -MeasureObjectNeighbors,6,Neighbors,cell,3,7,cell,3,2 +MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,8 +MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,9 +MeasureObjectNeighbors,6,Neighbors,cell,3,6,cell,3,10 MeasureObjectNeighbors,6,Neighbors,cell,3,7,cell,3,3 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MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,5 -MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,7 +MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,6 MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,9 -MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,12 +MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,10 +MeasureObjectNeighbors,6,Neighbors,cell,2,8,cell,2,11 +MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,1 +MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,3 MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,4 MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,5 MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,6 -MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,7 MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,8 MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,10 MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,11 -MeasureObjectNeighbors,6,Neighbors,cell,2,9,cell,2,12 +MeasureObjectNeighbors,6,Neighbors,cell,2,10,cell,2,1 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MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,2 MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,3 MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,4 MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,5 -MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,7 +MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,6 +MeasureObjectNeighbors,6,Neighbors,cell,4,1,cell,4,8 MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,1 MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,3 MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,4 MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,5 +MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,6 +MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,7 +MeasureObjectNeighbors,6,Neighbors,cell,4,2,cell,4,8 MeasureObjectNeighbors,6,Neighbors,cell,4,3,cell,4,1 MeasureObjectNeighbors,6,Neighbors,cell,4,3,cell,4,2 -MeasureObjectNeighbors,6,Neighbors,cell,4,3,cell,4,4 +MeasureObjectNeighbors,6,Neighbors,cell,4,3,cell,4,5 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MeasureObjectNeighbors,6,Neighbors,cell,12,2,cell,12,1 MeasureObjectNeighbors,6,Neighbors,cell,12,2,cell,12,3 -MeasureObjectNeighbors,6,Neighbors,cell,12,2,cell,12,6 +MeasureObjectNeighbors,6,Neighbors,cell,12,2,cell,12,5 MeasureObjectNeighbors,6,Neighbors,cell,12,3,cell,12,1 MeasureObjectNeighbors,6,Neighbors,cell,12,3,cell,12,2 -MeasureObjectNeighbors,6,Neighbors,cell,12,3,cell,12,6 -MeasureObjectNeighbors,6,Neighbors,cell,12,3,cell,12,11 -MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,5 +MeasureObjectNeighbors,6,Neighbors,cell,12,3,cell,12,5 +MeasureObjectNeighbors,6,Neighbors,cell,12,3,cell,12,12 +MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,6 MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,7 MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,9 MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,10 -MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,11 +MeasureObjectNeighbors,6,Neighbors,cell,12,4,cell,12,15 MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,1 -MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,4 +MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,2 +MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,3 MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,6 -MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,7 -MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,8 -MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,11 MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,12 MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,13 -MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,16 +MeasureObjectNeighbors,6,Neighbors,cell,12,5,cell,12,14 MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,1 -MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,2 -MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,3 +MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,4 MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,5 -MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,11 +MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,7 +MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,8 +MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,10 MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,12 MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,13 +MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,6,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,4 -MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,5 +MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,6 MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,9 MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,10 -MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,14 MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,7,cell,12,16 MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,4 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,5 +MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,6 MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,7 MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,9 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,12 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,14 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,10 +MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,13 MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,18 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,19 -MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,20 +MeasureObjectNeighbors,6,Neighbors,cell,12,8,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,4 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,7 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,10 -MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,11 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,15 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,18 +MeasureObjectNeighbors,6,Neighbors,cell,12,9,cell,12,19 MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,4 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,6 MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,7 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,9 -MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,13 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,16 MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,17 -MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,21 -MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,3 -MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,5 -MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,6 -MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,12 -MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,13 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,19 +MeasureObjectNeighbors,6,Neighbors,cell,12,10,cell,12,20 +MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,4 +MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,9 +MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,18 +MeasureObjectNeighbors,6,Neighbors,cell,12,11,cell,12,22 +MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,1 +MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,3 MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,5 MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,6 -MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,8 -MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,11 MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,13 -MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,15 -MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,18 -MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,19 +MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,17 +MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,23 +MeasureObjectNeighbors,6,Neighbors,cell,12,12,cell,12,24 MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,5 MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,6 -MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,11 +MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,8 +MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,10 MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,12 +MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,14 MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,19 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,4 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,7 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,8 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,9 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,10 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,17 +MeasureObjectNeighbors,6,Neighbors,cell,12,13,cell,12,20 +MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,5 +MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,6 +MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,12 +MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,13 MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,17 -MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,18 +MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,20 MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,21 +MeasureObjectNeighbors,6,Neighbors,cell,12,14,cell,12,23 +MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,4 MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,7 -MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,9 -MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,12 -MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,10 +MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,11 MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,18 MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,19 -MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,20 -MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,21 MeasureObjectNeighbors,6,Neighbors,cell,12,15,cell,12,22 -MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,5 +MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,7 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,9 -MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,12 +MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,10 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,13 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,18 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,19 MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,20 -MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,9 +MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,21 +MeasureObjectNeighbors,6,Neighbors,cell,12,16,cell,12,22 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,6 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,8 MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,10 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,12 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,13 MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,14 -MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,15 -MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,18 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,16 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,19 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,20 MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,21 -MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,22 -MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,8 +MeasureObjectNeighbors,6,Neighbors,cell,12,17,cell,12,23 MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,9 -MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,12 -MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,14 +MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,11 MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,15 MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,19 -MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,20 -MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,21 MeasureObjectNeighbors,6,Neighbors,cell,12,18,cell,12,22 -MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,8 -MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,12 -MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,13 +MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,9 +MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,10 MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,15 MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,16 +MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,18 MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,20 +MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,21 MeasureObjectNeighbors,6,Neighbors,cell,12,19,cell,12,22 -MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,8 -MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,10 +MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,13 +MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,14 MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,16 -MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,18 +MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,17 MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,19 MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,21 MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,22 -MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,10 +MeasureObjectNeighbors,6,Neighbors,cell,12,20,cell,12,23 MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,14 -MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,15 +MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,16 MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,17 -MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,18 +MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,19 MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,20 MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,22 +MeasureObjectNeighbors,6,Neighbors,cell,12,21,cell,12,23 +MeasureObjectNeighbors,6,Neighbors,cell,12,22,cell,12,11 MeasureObjectNeighbors,6,Neighbors,cell,12,22,cell,12,15 -MeasureObjectNeighbors,6,Neighbors,cell,12,22,cell,12,17 +MeasureObjectNeighbors,6,Neighbors,cell,12,22,cell,12,16 MeasureObjectNeighbors,6,Neighbors,cell,12,22,cell,12,18 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MeasureObjectNeighbors,6,Neighbors,cell,13,5,cell,13,7 MeasureObjectNeighbors,6,Neighbors,cell,13,5,cell,13,8 -MeasureObjectNeighbors,6,Neighbors,cell,13,5,cell,13,10 -MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,1 +MeasureObjectNeighbors,6,Neighbors,cell,13,5,cell,13,9 +MeasureObjectNeighbors,6,Neighbors,cell,13,5,cell,13,11 MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,3 MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,4 MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,5 @@ -724,7 +1095,6 @@ MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,9 MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,10 MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,11 MeasureObjectNeighbors,6,Neighbors,cell,13,6,cell,13,12 -MeasureObjectNeighbors,6,Neighbors,cell,13,7,cell,13,1 MeasureObjectNeighbors,6,Neighbors,cell,13,7,cell,13,2 MeasureObjectNeighbors,6,Neighbors,cell,13,7,cell,13,3 MeasureObjectNeighbors,6,Neighbors,cell,13,7,cell,13,4 @@ -735,82 +1105,153 @@ 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MeasureObjectNeighbors,6,Neighbors,cell,15,25,cell,15,26 MeasureObjectNeighbors,6,Neighbors,cell,15,25,cell,15,27 -MeasureObjectNeighbors,6,Neighbors,cell,15,25,cell,15,28 MeasureObjectNeighbors,6,Neighbors,cell,15,25,cell,15,29 MeasureObjectNeighbors,6,Neighbors,cell,15,25,cell,15,30 +MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,18 MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,19 -MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,21 -MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,22 +MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,20 MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,23 +MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,24 MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,25 +MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,27 MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,28 MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,29 MeasureObjectNeighbors,6,Neighbors,cell,15,26,cell,15,30 -MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,22 -MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,24 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,14 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,16 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,18 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,21 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,23 MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,25 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,26 MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,29 -MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,18 -MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,19 +MeasureObjectNeighbors,6,Neighbors,cell,15,27,cell,15,30 +MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,20 MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,22 MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,23 MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,24 -MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,25 MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,26 MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,29 MeasureObjectNeighbors,6,Neighbors,cell,15,28,cell,15,30 -MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,22 +MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,18 +MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,19 +MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,20 +MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,23 MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,24 MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,25 MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,26 MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,27 MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,28 MeasureObjectNeighbors,6,Neighbors,cell,15,29,cell,15,30 +MeasureObjectNeighbors,6,Neighbors,cell,15,30,cell,15,23 MeasureObjectNeighbors,6,Neighbors,cell,15,30,cell,15,25 MeasureObjectNeighbors,6,Neighbors,cell,15,30,cell,15,26 +MeasureObjectNeighbors,6,Neighbors,cell,15,30,cell,15,27 MeasureObjectNeighbors,6,Neighbors,cell,15,30,cell,15,28 MeasureObjectNeighbors,6,Neighbors,cell,15,30,cell,15,29 -MeasureObjectNeighbors,6,Neighbors,cell,14,1,cell,14,2 -MeasureObjectNeighbors,6,Neighbors,cell,14,1,cell,14,3 -MeasureObjectNeighbors,6,Neighbors,cell,14,1,cell,14,4 -MeasureObjectNeighbors,6,Neighbors,cell,14,1,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,1,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,2,cell,14,1 -MeasureObjectNeighbors,6,Neighbors,cell,14,2,cell,14,3 -MeasureObjectNeighbors,6,Neighbors,cell,14,2,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,2,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,2,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,3,cell,14,1 -MeasureObjectNeighbors,6,Neighbors,cell,14,3,cell,14,2 -MeasureObjectNeighbors,6,Neighbors,cell,14,3,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,3,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,3,cell,14,8 -MeasureObjectNeighbors,6,Neighbors,cell,14,3,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,4,cell,14,1 -MeasureObjectNeighbors,6,Neighbors,cell,14,4,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,4,cell,14,9 -MeasureObjectNeighbors,6,Neighbors,cell,14,4,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,4,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,1 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,2 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,4 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,9 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,5,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,1 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,2 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,3 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,8 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,12 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,6,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,2 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,3 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,8 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,12 -MeasureObjectNeighbors,6,Neighbors,cell,14,7,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,8,cell,14,3 -MeasureObjectNeighbors,6,Neighbors,cell,14,8,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,8,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,8,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,8,cell,14,12 -MeasureObjectNeighbors,6,Neighbors,cell,14,8,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,9,cell,14,4 -MeasureObjectNeighbors,6,Neighbors,cell,14,9,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,9,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,9,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,9,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,9,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,4 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,9 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,10,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,3 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,5 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,8 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,12 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,11,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,12,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,12,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,12,cell,14,8 -MeasureObjectNeighbors,6,Neighbors,cell,14,12,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,12,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,4 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,9 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,20 -MeasureObjectNeighbors,6,Neighbors,cell,14,13,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,7 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,8 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,12 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,14,cell,14,25 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,9 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,15,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,6 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,11 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,16,cell,14,25 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,17,cell,14,25 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,9 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,10 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,20 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,18,cell,14,27 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,15 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,19,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,20,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,20,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,20,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,20,cell,14,22 -MeasureObjectNeighbors,6,Neighbors,cell,14,20,cell,14,24 -MeasureObjectNeighbors,6,Neighbors,cell,14,20,cell,14,28 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,13 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,20 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,24 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,21,cell,14,27 -MeasureObjectNeighbors,6,Neighbors,cell,14,22,cell,14,20 -MeasureObjectNeighbors,6,Neighbors,cell,14,22,cell,14,24 -MeasureObjectNeighbors,6,Neighbors,cell,14,22,cell,14,28 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,25 -MeasureObjectNeighbors,6,Neighbors,cell,14,23,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,24,cell,14,20 -MeasureObjectNeighbors,6,Neighbors,cell,14,24,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,24,cell,14,22 -MeasureObjectNeighbors,6,Neighbors,cell,14,24,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,24,cell,14,27 -MeasureObjectNeighbors,6,Neighbors,cell,14,24,cell,14,28 -MeasureObjectNeighbors,6,Neighbors,cell,14,25,cell,14,14 -MeasureObjectNeighbors,6,Neighbors,cell,14,25,cell,14,16 -MeasureObjectNeighbors,6,Neighbors,cell,14,25,cell,14,17 -MeasureObjectNeighbors,6,Neighbors,cell,14,25,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,25,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,19 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,23 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,24 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,25 -MeasureObjectNeighbors,6,Neighbors,cell,14,26,cell,14,27 -MeasureObjectNeighbors,6,Neighbors,cell,14,27,cell,14,18 -MeasureObjectNeighbors,6,Neighbors,cell,14,27,cell,14,21 -MeasureObjectNeighbors,6,Neighbors,cell,14,27,cell,14,24 -MeasureObjectNeighbors,6,Neighbors,cell,14,27,cell,14,26 -MeasureObjectNeighbors,6,Neighbors,cell,14,27,cell,14,28 -MeasureObjectNeighbors,6,Neighbors,cell,14,28,cell,14,20 -MeasureObjectNeighbors,6,Neighbors,cell,14,28,cell,14,22 -MeasureObjectNeighbors,6,Neighbors,cell,14,28,cell,14,24 -MeasureObjectNeighbors,6,Neighbors,cell,14,28,cell,14,27 diff --git a/inst/extdata/mockData/cpout/cell.csv b/inst/extdata/mockData/cpout/cell.csv index 01f4dff..74ee770 100644 --- a/inst/extdata/mockData/cpout/cell.csv +++ b/inst/extdata/mockData/cpout/cell.csv @@ -1,210 +1,240 @@ ImageNumber,ObjectNumber,AreaShape_Area,AreaShape_BoundingBoxArea,AreaShape_BoundingBoxMaximum_X,AreaShape_BoundingBoxMaximum_Y,AreaShape_BoundingBoxMinimum_X,AreaShape_BoundingBoxMinimum_Y,AreaShape_Center_X,AreaShape_Center_Y,AreaShape_Compactness,AreaShape_ConvexArea,AreaShape_Eccentricity,AreaShape_EquivalentDiameter,AreaShape_EulerNumber,AreaShape_Extent,AreaShape_FormFactor,AreaShape_MajorAxisLength,AreaShape_MaxFeretDiameter,AreaShape_MaximumRadius,AreaShape_MeanRadius,AreaShape_MedianRadius,AreaShape_MinFeretDiameter,AreaShape_MinorAxisLength,AreaShape_Orientation,AreaShape_Perimeter,AreaShape_Solidity,Intensity_IntegratedIntensityEdge_FullStack_c1,Intensity_IntegratedIntensityEdge_FullStack_c2,Intensity_IntegratedIntensityEdge_FullStack_c3,Intensity_IntegratedIntensityEdge_FullStack_c4,Intensity_IntegratedIntensityEdge_FullStack_c5,Intensity_IntegratedIntensityEdge_ProbabStack_c1,Intensity_IntegratedIntensityEdge_ProbabStack_c2,Intensity_IntegratedIntensityEdge_ProbabStack_c3,Intensity_IntegratedIntensity_FullStack_c1,Intensity_IntegratedIntensity_FullStack_c2,Intensity_IntegratedIntensity_FullStack_c3,Intensity_IntegratedIntensity_FullStack_c4,Intensity_IntegratedIntensity_FullStack_c5,Intensity_IntegratedIntensity_ProbabStack_c1,Intensity_IntegratedIntensity_ProbabStack_c2,Intensity_IntegratedIntensity_ProbabStack_c3,Intensity_LowerQuartileIntensity_FullStack_c1,Intensity_LowerQuartileIntensity_FullStack_c2,Intensity_LowerQuartileIntensity_FullStack_c3,Intensity_LowerQuartileIntensity_FullStack_c4,Intensity_LowerQuartileIntensity_FullStack_c5,Intensity_LowerQuartileIntensity_ProbabStack_c1,Intensity_LowerQuartileIntensity_ProbabStack_c2,Intensity_LowerQuartileIntensity_ProbabStack_c3,Intensity_MADIntensity_FullStack_c1,Intensity_MADIntensity_FullStack_c2,Intensity_MADIntensity_FullStack_c3,Intensity_MADIntensity_FullStack_c4,Intensity_MADIntensity_FullStack_c5,Intensity_MADIntensity_ProbabStack_c1,Intensity_MADIntensity_ProbabStack_c2,Intensity_MADIntensity_ProbabStack_c3,Intensity_MassDisplacement_FullStack_c1,Intensity_MassDisplacement_FullStack_c2,Intensity_MassDisplacement_FullStack_c3,Intensity_MassDisplacement_FullStack_c4,Intensity_MassDisplacement_FullStack_c5,Intensity_MassDisplacement_ProbabStack_c1,Intensity_MassDisplacement_ProbabStack_c2,Intensity_MassDisplacement_ProbabStack_c3,Intensity_MaxIntensityEdge_FullStack_c1,Intensity_MaxIntensityEdge_FullStack_c2,Intensity_MaxIntensityEdge_FullStack_c3,Intensity_MaxIntensityEdge_FullStack_c4,Intensity_MaxIntensityEdge_FullStack_c5,Intensity_MaxIntensityEdge_ProbabStack_c1,Intensity_MaxIntensityEdge_ProbabStack_c2,Intensity_MaxIntensityEdge_ProbabStack_c3,Intensity_MaxIntensity_FullStack_c1,Intensity_MaxIntensity_FullStack_c2,Intensity_MaxIntensity_FullStack_c3,Intensity_MaxIntensity_FullStack_c4,Intensity_MaxIntensity_FullStack_c5,Intensity_MaxIntensity_ProbabStack_c1,Intensity_MaxIntensity_ProbabStack_c2,Intensity_MaxIntensity_ProbabStack_c3,Intensity_MeanIntensityEdge_FullStack_c1,Intensity_MeanIntensityEdge_FullStack_c2,Intensity_MeanIntensityEdge_FullStack_c3,Intensity_MeanIntensityEdge_FullStack_c4,Intensity_MeanIntensityEdge_FullStack_c5,Intensity_MeanIntensityEdge_ProbabStack_c1,Intensity_MeanIntensityEdge_ProbabStack_c2,Intensity_MeanIntensityEdge_ProbabStack_c3,Intensity_MeanIntensity_FullStack_c1,Intensity_MeanIntensity_FullStack_c2,Intensity_MeanIntensity_FullStack_c3,Intensity_MeanIntensity_FullStack_c4,Intensity_MeanIntensity_FullStack_c5,Intensity_MeanIntensity_ProbabStack_c1,Intensity_MeanIntensity_ProbabStack_c2,Intensity_MeanIntensity_ProbabStack_c3,Intensity_MedianIntensity_FullStack_c1,Intensity_MedianIntensity_FullStack_c2,Intensity_MedianIntensity_FullStack_c3,Intensity_MedianIntensity_FullStack_c4,Intensity_MedianIntensity_FullStack_c5,Intensity_MedianIntensity_ProbabStack_c1,Intensity_MedianIntensity_ProbabStack_c2,Intensity_MedianIntensity_ProbabStack_c3,Intensity_MinIntensityEdge_FullStack_c1,Intensity_MinIntensityEdge_FullStack_c2,Intensity_MinIntensityEdge_FullStack_c3,Intensity_MinIntensityEdge_FullStack_c4,Intensity_MinIntensityEdge_FullStack_c5,Intensity_MinIntensityEdge_ProbabStack_c1,Intensity_MinIntensityEdge_ProbabStack_c2,Intensity_MinIntensityEdge_ProbabStack_c3,Intensity_MinIntensity_FullStack_c1,Intensity_MinIntensity_FullStack_c2,Intensity_MinIntensity_FullStack_c3,Intensity_MinIntensity_FullStack_c4,Intensity_MinIntensity_FullStack_c5,Intensity_MinIntensity_ProbabStack_c1,Intensity_MinIntensity_ProbabStack_c2,Intensity_MinIntensity_ProbabStack_c3,Intensity_StdIntensityEdge_FullStack_c1,Intensity_StdIntensityEdge_FullStack_c2,Intensity_StdIntensityEdge_FullStack_c3,Intensity_StdIntensityEdge_FullStack_c4,Intensity_StdIntensityEdge_FullStack_c5,Intensity_StdIntensityEdge_ProbabStack_c1,Intensity_StdIntensityEdge_ProbabStack_c2,Intensity_StdIntensityEdge_ProbabStack_c3,Intensity_StdIntensity_FullStack_c1,Intensity_StdIntensity_FullStack_c2,Intensity_StdIntensity_FullStack_c3,Intensity_StdIntensity_FullS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diff --git a/inst/extdata/mockData/cpout/panel.csv b/inst/extdata/mockData/cpout/panel.csv index b982322..b841640 100644 --- a/inst/extdata/mockData/cpout/panel.csv +++ b/inst/extdata/mockData/cpout/panel.csv @@ -1,6 +1,6 @@ -Tube Number,Metal Tag,Target,ilastik,full -625,Sm147,Laminin,0,1 -1378,Yb172,H3K27Ac,1,1 -2266,Pr141,Cytokeratin 5,0,1 -2359,Eu153,YBX1,1,1 -,Ag107,Ag107,1,1 \ No newline at end of file +Tube Number,Metal Tag,Target,ilastik,full,deepcell,cellpose +625,Sm147,Laminin,0,1,, +1378,Yb172,H3K27Ac,1,1,1,1 +2266,Pr141,Cytokeratin 5,0,1,2,2 +2359,Eu153,YBX1,1,1,, +,Ag107,Ag107,1,1,, \ No newline at end of file diff --git a/inst/extdata/mockData/cpout/var_Image.csv b/inst/extdata/mockData/cpout/var_Image.csv index 862fb1e..0e0771e 100644 --- a/inst/extdata/mockData/cpout/var_Image.csv +++ b/inst/extdata/mockData/cpout/var_Image.csv @@ -80,39 +80,39 @@ ModuleError_08MeasureObjectIntensityMultichannel,Execution,,,ModuleError,,08Meas ExecutionTime_08MeasureObjectIntensityMultichannel,Execution,,,ExecutionTime,,08MeasureObjectIntensityMultichannel,,float ModuleError_09MeasureObjectSizeShape,Execution,,,ModuleError,,09MeasureObjectSizeShape,,integer ExecutionTime_09MeasureObjectSizeShape,Execution,,,ExecutionTime,,09MeasureObjectSizeShape,,float -Intensity_TotalIntensity_FullStack_c1,Intensity,FullStack,,TotalIntensity,1,,Sm147,float -Intensity_MeanIntensity_FullStack_c1,Intensity,FullStack,,MeanIntensity,1,,Sm147,float -Intensity_MedianIntensity_FullStack_c1,Intensity,FullStack,,MedianIntensity,1,,Sm147,float -Intensity_StdIntensity_FullStack_c1,Intensity,FullStack,,StdIntensity,1,,Sm147,float -Intensity_MADIntensity_FullStack_c1,Intensity,FullStack,,MADIntensity,1,,Sm147,float -Intensity_MinIntensity_FullStack_c1,Intensity,FullStack,,MinIntensity,1,,Sm147,float -Intensity_MaxIntensity_FullStack_c1,Intensity,FullStack,,MaxIntensity,1,,Sm147,float -Intensity_TotalArea_FullStack_c1,Intensity,FullStack,,TotalArea,1,,Sm147,integer -Intensity_PercentMaximal_FullStack_c1,Intensity,FullStack,,PercentMaximal,1,,Sm147,float -Intensity_LowerQuartileIntensity_FullStack_c1,Intensity,FullStack,,LowerQuartileIntensity,1,,Sm147,float -Intensity_UpperQuartileIntensity_FullStack_c1,Intensity,FullStack,,UpperQuartileIntensity,1,,Sm147,float -Intensity_TotalIntensity_FullStack_c2,Intensity,FullStack,,TotalIntensity,2,,Yb172,float -Intensity_MeanIntensity_FullStack_c2,Intensity,FullStack,,MeanIntensity,2,,Yb172,float -Intensity_MedianIntensity_FullStack_c2,Intensity,FullStack,,MedianIntensity,2,,Yb172,float -Intensity_StdIntensity_FullStack_c2,Intensity,FullStack,,StdIntensity,2,,Yb172,float -Intensity_MADIntensity_FullStack_c2,Intensity,FullStack,,MADIntensity,2,,Yb172,float -Intensity_MinIntensity_FullStack_c2,Intensity,FullStack,,MinIntensity,2,,Yb172,float -Intensity_MaxIntensity_FullStack_c2,Intensity,FullStack,,MaxIntensity,2,,Yb172,float -Intensity_TotalArea_FullStack_c2,Intensity,FullStack,,TotalArea,2,,Yb172,integer -Intensity_PercentMaximal_FullStack_c2,Intensity,FullStack,,PercentMaximal,2,,Yb172,float -Intensity_LowerQuartileIntensity_FullStack_c2,Intensity,FullStack,,LowerQuartileIntensity,2,,Yb172,float -Intensity_UpperQuartileIntensity_FullStack_c2,Intensity,FullStack,,UpperQuartileIntensity,2,,Yb172,float -Intensity_TotalIntensity_FullStack_c3,Intensity,FullStack,,TotalIntensity,3,,Pr141,float -Intensity_MeanIntensity_FullStack_c3,Intensity,FullStack,,MeanIntensity,3,,Pr141,float -Intensity_MedianIntensity_FullStack_c3,Intensity,FullStack,,MedianIntensity,3,,Pr141,float -Intensity_StdIntensity_FullStack_c3,Intensity,FullStack,,StdIntensity,3,,Pr141,float -Intensity_MADIntensity_FullStack_c3,Intensity,FullStack,,MADIntensity,3,,Pr141,float -Intensity_MinIntensity_FullStack_c3,Intensity,FullStack,,MinIntensity,3,,Pr141,float -Intensity_MaxIntensity_FullStack_c3,Intensity,FullStack,,MaxIntensity,3,,Pr141,float -Intensity_TotalArea_FullStack_c3,Intensity,FullStack,,TotalArea,3,,Pr141,integer -Intensity_PercentMaximal_FullStack_c3,Intensity,FullStack,,PercentMaximal,3,,Pr141,float -Intensity_LowerQuartileIntensity_FullStack_c3,Intensity,FullStack,,LowerQuartileIntensity,3,,Pr141,float -Intensity_UpperQuartileIntensity_FullStack_c3,Intensity,FullStack,,UpperQuartileIntensity,3,,Pr141,float +Intensity_TotalIntensity_FullStack_c1,Intensity,FullStack,,TotalIntensity,1,,Ag107,float +Intensity_MeanIntensity_FullStack_c1,Intensity,FullStack,,MeanIntensity,1,,Ag107,float +Intensity_MedianIntensity_FullStack_c1,Intensity,FullStack,,MedianIntensity,1,,Ag107,float +Intensity_StdIntensity_FullStack_c1,Intensity,FullStack,,StdIntensity,1,,Ag107,float +Intensity_MADIntensity_FullStack_c1,Intensity,FullStack,,MADIntensity,1,,Ag107,float +Intensity_MinIntensity_FullStack_c1,Intensity,FullStack,,MinIntensity,1,,Ag107,float +Intensity_MaxIntensity_FullStack_c1,Intensity,FullStack,,MaxIntensity,1,,Ag107,float +Intensity_TotalArea_FullStack_c1,Intensity,FullStack,,TotalArea,1,,Ag107,integer +Intensity_PercentMaximal_FullStack_c1,Intensity,FullStack,,PercentMaximal,1,,Ag107,float +Intensity_LowerQuartileIntensity_FullStack_c1,Intensity,FullStack,,LowerQuartileIntensity,1,,Ag107,float +Intensity_UpperQuartileIntensity_FullStack_c1,Intensity,FullStack,,UpperQuartileIntensity,1,,Ag107,float +Intensity_TotalIntensity_FullStack_c2,Intensity,FullStack,,TotalIntensity,2,,Pr141,float +Intensity_MeanIntensity_FullStack_c2,Intensity,FullStack,,MeanIntensity,2,,Pr141,float +Intensity_MedianIntensity_FullStack_c2,Intensity,FullStack,,MedianIntensity,2,,Pr141,float +Intensity_StdIntensity_FullStack_c2,Intensity,FullStack,,StdIntensity,2,,Pr141,float +Intensity_MADIntensity_FullStack_c2,Intensity,FullStack,,MADIntensity,2,,Pr141,float +Intensity_MinIntensity_FullStack_c2,Intensity,FullStack,,MinIntensity,2,,Pr141,float +Intensity_MaxIntensity_FullStack_c2,Intensity,FullStack,,MaxIntensity,2,,Pr141,float +Intensity_TotalArea_FullStack_c2,Intensity,FullStack,,TotalArea,2,,Pr141,integer +Intensity_PercentMaximal_FullStack_c2,Intensity,FullStack,,PercentMaximal,2,,Pr141,float +Intensity_LowerQuartileIntensity_FullStack_c2,Intensity,FullStack,,LowerQuartileIntensity,2,,Pr141,float +Intensity_UpperQuartileIntensity_FullStack_c2,Intensity,FullStack,,UpperQuartileIntensity,2,,Pr141,float +Intensity_TotalIntensity_FullStack_c3,Intensity,FullStack,,TotalIntensity,3,,Sm147,float +Intensity_MeanIntensity_FullStack_c3,Intensity,FullStack,,MeanIntensity,3,,Sm147,float +Intensity_MedianIntensity_FullStack_c3,Intensity,FullStack,,MedianIntensity,3,,Sm147,float +Intensity_StdIntensity_FullStack_c3,Intensity,FullStack,,StdIntensity,3,,Sm147,float +Intensity_MADIntensity_FullStack_c3,Intensity,FullStack,,MADIntensity,3,,Sm147,float +Intensity_MinIntensity_FullStack_c3,Intensity,FullStack,,MinIntensity,3,,Sm147,float +Intensity_MaxIntensity_FullStack_c3,Intensity,FullStack,,MaxIntensity,3,,Sm147,float +Intensity_TotalArea_FullStack_c3,Intensity,FullStack,,TotalArea,3,,Sm147,integer +Intensity_PercentMaximal_FullStack_c3,Intensity,FullStack,,PercentMaximal,3,,Sm147,float +Intensity_LowerQuartileIntensity_FullStack_c3,Intensity,FullStack,,LowerQuartileIntensity,3,,Sm147,float +Intensity_UpperQuartileIntensity_FullStack_c3,Intensity,FullStack,,UpperQuartileIntensity,3,,Sm147,float Intensity_TotalIntensity_FullStack_c4,Intensity,FullStack,,TotalIntensity,4,,Eu153,float Intensity_MeanIntensity_FullStack_c4,Intensity,FullStack,,MeanIntensity,4,,Eu153,float Intensity_MedianIntensity_FullStack_c4,Intensity,FullStack,,MedianIntensity,4,,Eu153,float @@ -124,17 +124,17 @@ Intensity_TotalArea_FullStack_c4,Intensity,FullStack,,TotalArea,4,,Eu153,integer Intensity_PercentMaximal_FullStack_c4,Intensity,FullStack,,PercentMaximal,4,,Eu153,float Intensity_LowerQuartileIntensity_FullStack_c4,Intensity,FullStack,,LowerQuartileIntensity,4,,Eu153,float Intensity_UpperQuartileIntensity_FullStack_c4,Intensity,FullStack,,UpperQuartileIntensity,4,,Eu153,float -Intensity_TotalIntensity_FullStack_c5,Intensity,FullStack,,TotalIntensity,5,,Ag107,float -Intensity_MeanIntensity_FullStack_c5,Intensity,FullStack,,MeanIntensity,5,,Ag107,float -Intensity_MedianIntensity_FullStack_c5,Intensity,FullStack,,MedianIntensity,5,,Ag107,float -Intensity_StdIntensity_FullStack_c5,Intensity,FullStack,,StdIntensity,5,,Ag107,float -Intensity_MADIntensity_FullStack_c5,Intensity,FullStack,,MADIntensity,5,,Ag107,float -Intensity_MinIntensity_FullStack_c5,Intensity,FullStack,,MinIntensity,5,,Ag107,float -Intensity_MaxIntensity_FullStack_c5,Intensity,FullStack,,MaxIntensity,5,,Ag107,float -Intensity_TotalArea_FullStack_c5,Intensity,FullStack,,TotalArea,5,,Ag107,integer -Intensity_PercentMaximal_FullStack_c5,Intensity,FullStack,,PercentMaximal,5,,Ag107,float -Intensity_LowerQuartileIntensity_FullStack_c5,Intensity,FullStack,,LowerQuartileIntensity,5,,Ag107,float -Intensity_UpperQuartileIntensity_FullStack_c5,Intensity,FullStack,,UpperQuartileIntensity,5,,Ag107,float +Intensity_TotalIntensity_FullStack_c5,Intensity,FullStack,,TotalIntensity,5,,Yb172,float +Intensity_MeanIntensity_FullStack_c5,Intensity,FullStack,,MeanIntensity,5,,Yb172,float +Intensity_MedianIntensity_FullStack_c5,Intensity,FullStack,,MedianIntensity,5,,Yb172,float +Intensity_StdIntensity_FullStack_c5,Intensity,FullStack,,StdIntensity,5,,Yb172,float +Intensity_MADIntensity_FullStack_c5,Intensity,FullStack,,MADIntensity,5,,Yb172,float +Intensity_MinIntensity_FullStack_c5,Intensity,FullStack,,MinIntensity,5,,Yb172,float +Intensity_MaxIntensity_FullStack_c5,Intensity,FullStack,,MaxIntensity,5,,Yb172,float +Intensity_TotalArea_FullStack_c5,Intensity,FullStack,,TotalArea,5,,Yb172,integer +Intensity_PercentMaximal_FullStack_c5,Intensity,FullStack,,PercentMaximal,5,,Yb172,float +Intensity_LowerQuartileIntensity_FullStack_c5,Intensity,FullStack,,LowerQuartileIntensity,5,,Yb172,float +Intensity_UpperQuartileIntensity_FullStack_c5,Intensity,FullStack,,UpperQuartileIntensity,5,,Yb172,float ModuleError_10MeasureImageIntensityMultichannel,Execution,,,ModuleError,,10MeasureImageIntensityMultichannel,,integer ExecutionTime_10MeasureImageIntensityMultichannel,Execution,,,ExecutionTime,,10MeasureImageIntensityMultichannel,,float Intensity_TotalIntensity_ProbabStack_c1,Intensity,ProbabStack,,TotalIntensity,1,,CellCenter,float diff --git a/inst/extdata/mockData/cpout/var_cell.csv b/inst/extdata/mockData/cpout/var_cell.csv index 7447412..86f1402 100644 --- a/inst/extdata/mockData/cpout/var_cell.csv +++ b/inst/extdata/mockData/cpout/var_cell.csv @@ -10,69 +10,69 @@ Neighbors_FirstClosestDistance_8,Neighbors,,,FirstClosestDistance,,8,,float Neighbors_SecondClosestObjectNumber_8,Neighbors,,,SecondClosestObjectNumber,,8,,integer Neighbors_SecondClosestDistance_8,Neighbors,,,SecondClosestDistance,,8,,float Neighbors_AngleBetweenNeighbors_8,Neighbors,,,AngleBetweenNeighbors,,8,,float -Intensity_IntegratedIntensity_FullStack_c1,Intensity,FullStack,,IntegratedIntensity,1,,Sm147,float -Intensity_MeanIntensity_FullStack_c1,Intensity,FullStack,,MeanIntensity,1,,Sm147,float -Intensity_StdIntensity_FullStack_c1,Intensity,FullStack,,StdIntensity,1,,Sm147,float -Intensity_MinIntensity_FullStack_c1,Intensity,FullStack,,MinIntensity,1,,Sm147,float -Intensity_MaxIntensity_FullStack_c1,Intensity,FullStack,,MaxIntensity,1,,Sm147,float -Intensity_IntegratedIntensityEdge_FullStack_c1,Intensity,FullStack,,IntegratedIntensityEdge,1,,Sm147,float -Intensity_MeanIntensityEdge_FullStack_c1,Intensity,FullStack,,MeanIntensityEdge,1,,Sm147,float -Intensity_StdIntensityEdge_FullStack_c1,Intensity,FullStack,,StdIntensityEdge,1,,Sm147,float -Intensity_MinIntensityEdge_FullStack_c1,Intensity,FullStack,,MinIntensityEdge,1,,Sm147,float -Intensity_MaxIntensityEdge_FullStack_c1,Intensity,FullStack,,MaxIntensityEdge,1,,Sm147,float -Intensity_MassDisplacement_FullStack_c1,Intensity,FullStack,,MassDisplacement,1,,Sm147,float -Intensity_LowerQuartileIntensity_FullStack_c1,Intensity,FullStack,,LowerQuartileIntensity,1,,Sm147,float -Intensity_MedianIntensity_FullStack_c1,Intensity,FullStack,,MedianIntensity,1,,Sm147,float -Intensity_MADIntensity_FullStack_c1,Intensity,FullStack,,MADIntensity,1,,Sm147,float -Intensity_UpperQuartileIntensity_FullStack_c1,Intensity,FullStack,,UpperQuartileIntensity,1,,Sm147,float -Location_CenterMassIntensity_X_FullStack_c1,Location,FullStack,,CenterMassIntensity_X,1,,Sm147,float -Location_CenterMassIntensity_Y_FullStack_c1,Location,FullStack,,CenterMassIntensity_Y,1,,Sm147,float -Location_CenterMassIntensity_Z_FullStack_c1,Location,FullStack,,CenterMassIntensity_Z,1,,Sm147,float -Location_MaxIntensity_X_FullStack_c1,Location,FullStack,,MaxIntensity_X,1,,Sm147,float -Location_MaxIntensity_Y_FullStack_c1,Location,FullStack,,MaxIntensity_Y,1,,Sm147,float -Location_MaxIntensity_Z_FullStack_c1,Location,FullStack,,MaxIntensity_Z,1,,Sm147,float -Intensity_IntegratedIntensity_FullStack_c2,Intensity,FullStack,,IntegratedIntensity,2,,Yb172,float -Intensity_MeanIntensity_FullStack_c2,Intensity,FullStack,,MeanIntensity,2,,Yb172,float -Intensity_StdIntensity_FullStack_c2,Intensity,FullStack,,StdIntensity,2,,Yb172,float -Intensity_MinIntensity_FullStack_c2,Intensity,FullStack,,MinIntensity,2,,Yb172,float -Intensity_MaxIntensity_FullStack_c2,Intensity,FullStack,,MaxIntensity,2,,Yb172,float -Intensity_IntegratedIntensityEdge_FullStack_c2,Intensity,FullStack,,IntegratedIntensityEdge,2,,Yb172,float -Intensity_MeanIntensityEdge_FullStack_c2,Intensity,FullStack,,MeanIntensityEdge,2,,Yb172,float -Intensity_StdIntensityEdge_FullStack_c2,Intensity,FullStack,,StdIntensityEdge,2,,Yb172,float -Intensity_MinIntensityEdge_FullStack_c2,Intensity,FullStack,,MinIntensityEdge,2,,Yb172,float -Intensity_MaxIntensityEdge_FullStack_c2,Intensity,FullStack,,MaxIntensityEdge,2,,Yb172,float -Intensity_MassDisplacement_FullStack_c2,Intensity,FullStack,,MassDisplacement,2,,Yb172,float -Intensity_LowerQuartileIntensity_FullStack_c2,Intensity,FullStack,,LowerQuartileIntensity,2,,Yb172,float -Intensity_MedianIntensity_FullStack_c2,Intensity,FullStack,,MedianIntensity,2,,Yb172,float -Intensity_MADIntensity_FullStack_c2,Intensity,FullStack,,MADIntensity,2,,Yb172,float -Intensity_UpperQuartileIntensity_FullStack_c2,Intensity,FullStack,,UpperQuartileIntensity,2,,Yb172,float -Location_CenterMassIntensity_X_FullStack_c2,Location,FullStack,,CenterMassIntensity_X,2,,Yb172,float -Location_CenterMassIntensity_Y_FullStack_c2,Location,FullStack,,CenterMassIntensity_Y,2,,Yb172,float -Location_CenterMassIntensity_Z_FullStack_c2,Location,FullStack,,CenterMassIntensity_Z,2,,Yb172,float -Location_MaxIntensity_X_FullStack_c2,Location,FullStack,,MaxIntensity_X,2,,Yb172,float -Location_MaxIntensity_Y_FullStack_c2,Location,FullStack,,MaxIntensity_Y,2,,Yb172,float -Location_MaxIntensity_Z_FullStack_c2,Location,FullStack,,MaxIntensity_Z,2,,Yb172,float -Intensity_IntegratedIntensity_FullStack_c3,Intensity,FullStack,,IntegratedIntensity,3,,Pr141,float -Intensity_MeanIntensity_FullStack_c3,Intensity,FullStack,,MeanIntensity,3,,Pr141,float -Intensity_StdIntensity_FullStack_c3,Intensity,FullStack,,StdIntensity,3,,Pr141,float -Intensity_MinIntensity_FullStack_c3,Intensity,FullStack,,MinIntensity,3,,Pr141,float -Intensity_MaxIntensity_FullStack_c3,Intensity,FullStack,,MaxIntensity,3,,Pr141,float -Intensity_IntegratedIntensityEdge_FullStack_c3,Intensity,FullStack,,IntegratedIntensityEdge,3,,Pr141,float -Intensity_MeanIntensityEdge_FullStack_c3,Intensity,FullStack,,MeanIntensityEdge,3,,Pr141,float -Intensity_StdIntensityEdge_FullStack_c3,Intensity,FullStack,,StdIntensityEdge,3,,Pr141,float -Intensity_MinIntensityEdge_FullStack_c3,Intensity,FullStack,,MinIntensityEdge,3,,Pr141,float -Intensity_MaxIntensityEdge_FullStack_c3,Intensity,FullStack,,MaxIntensityEdge,3,,Pr141,float -Intensity_MassDisplacement_FullStack_c3,Intensity,FullStack,,MassDisplacement,3,,Pr141,float -Intensity_LowerQuartileIntensity_FullStack_c3,Intensity,FullStack,,LowerQuartileIntensity,3,,Pr141,float -Intensity_MedianIntensity_FullStack_c3,Intensity,FullStack,,MedianIntensity,3,,Pr141,float -Intensity_MADIntensity_FullStack_c3,Intensity,FullStack,,MADIntensity,3,,Pr141,float -Intensity_UpperQuartileIntensity_FullStack_c3,Intensity,FullStack,,UpperQuartileIntensity,3,,Pr141,float -Location_CenterMassIntensity_X_FullStack_c3,Location,FullStack,,CenterMassIntensity_X,3,,Pr141,float -Location_CenterMassIntensity_Y_FullStack_c3,Location,FullStack,,CenterMassIntensity_Y,3,,Pr141,float -Location_CenterMassIntensity_Z_FullStack_c3,Location,FullStack,,CenterMassIntensity_Z,3,,Pr141,float -Location_MaxIntensity_X_FullStack_c3,Location,FullStack,,MaxIntensity_X,3,,Pr141,float -Location_MaxIntensity_Y_FullStack_c3,Location,FullStack,,MaxIntensity_Y,3,,Pr141,float -Location_MaxIntensity_Z_FullStack_c3,Location,FullStack,,MaxIntensity_Z,3,,Pr141,float +Intensity_IntegratedIntensity_FullStack_c1,Intensity,FullStack,,IntegratedIntensity,1,,Ag107,float +Intensity_MeanIntensity_FullStack_c1,Intensity,FullStack,,MeanIntensity,1,,Ag107,float +Intensity_StdIntensity_FullStack_c1,Intensity,FullStack,,StdIntensity,1,,Ag107,float +Intensity_MinIntensity_FullStack_c1,Intensity,FullStack,,MinIntensity,1,,Ag107,float +Intensity_MaxIntensity_FullStack_c1,Intensity,FullStack,,MaxIntensity,1,,Ag107,float +Intensity_IntegratedIntensityEdge_FullStack_c1,Intensity,FullStack,,IntegratedIntensityEdge,1,,Ag107,float +Intensity_MeanIntensityEdge_FullStack_c1,Intensity,FullStack,,MeanIntensityEdge,1,,Ag107,float +Intensity_StdIntensityEdge_FullStack_c1,Intensity,FullStack,,StdIntensityEdge,1,,Ag107,float +Intensity_MinIntensityEdge_FullStack_c1,Intensity,FullStack,,MinIntensityEdge,1,,Ag107,float +Intensity_MaxIntensityEdge_FullStack_c1,Intensity,FullStack,,MaxIntensityEdge,1,,Ag107,float +Intensity_MassDisplacement_FullStack_c1,Intensity,FullStack,,MassDisplacement,1,,Ag107,float +Intensity_LowerQuartileIntensity_FullStack_c1,Intensity,FullStack,,LowerQuartileIntensity,1,,Ag107,float +Intensity_MedianIntensity_FullStack_c1,Intensity,FullStack,,MedianIntensity,1,,Ag107,float +Intensity_MADIntensity_FullStack_c1,Intensity,FullStack,,MADIntensity,1,,Ag107,float +Intensity_UpperQuartileIntensity_FullStack_c1,Intensity,FullStack,,UpperQuartileIntensity,1,,Ag107,float +Location_CenterMassIntensity_X_FullStack_c1,Location,FullStack,,CenterMassIntensity_X,1,,Ag107,float +Location_CenterMassIntensity_Y_FullStack_c1,Location,FullStack,,CenterMassIntensity_Y,1,,Ag107,float +Location_CenterMassIntensity_Z_FullStack_c1,Location,FullStack,,CenterMassIntensity_Z,1,,Ag107,float +Location_MaxIntensity_X_FullStack_c1,Location,FullStack,,MaxIntensity_X,1,,Ag107,float +Location_MaxIntensity_Y_FullStack_c1,Location,FullStack,,MaxIntensity_Y,1,,Ag107,float +Location_MaxIntensity_Z_FullStack_c1,Location,FullStack,,MaxIntensity_Z,1,,Ag107,float +Intensity_IntegratedIntensity_FullStack_c2,Intensity,FullStack,,IntegratedIntensity,2,,Pr141,float +Intensity_MeanIntensity_FullStack_c2,Intensity,FullStack,,MeanIntensity,2,,Pr141,float +Intensity_StdIntensity_FullStack_c2,Intensity,FullStack,,StdIntensity,2,,Pr141,float +Intensity_MinIntensity_FullStack_c2,Intensity,FullStack,,MinIntensity,2,,Pr141,float +Intensity_MaxIntensity_FullStack_c2,Intensity,FullStack,,MaxIntensity,2,,Pr141,float +Intensity_IntegratedIntensityEdge_FullStack_c2,Intensity,FullStack,,IntegratedIntensityEdge,2,,Pr141,float +Intensity_MeanIntensityEdge_FullStack_c2,Intensity,FullStack,,MeanIntensityEdge,2,,Pr141,float +Intensity_StdIntensityEdge_FullStack_c2,Intensity,FullStack,,StdIntensityEdge,2,,Pr141,float +Intensity_MinIntensityEdge_FullStack_c2,Intensity,FullStack,,MinIntensityEdge,2,,Pr141,float +Intensity_MaxIntensityEdge_FullStack_c2,Intensity,FullStack,,MaxIntensityEdge,2,,Pr141,float +Intensity_MassDisplacement_FullStack_c2,Intensity,FullStack,,MassDisplacement,2,,Pr141,float +Intensity_LowerQuartileIntensity_FullStack_c2,Intensity,FullStack,,LowerQuartileIntensity,2,,Pr141,float +Intensity_MedianIntensity_FullStack_c2,Intensity,FullStack,,MedianIntensity,2,,Pr141,float +Intensity_MADIntensity_FullStack_c2,Intensity,FullStack,,MADIntensity,2,,Pr141,float +Intensity_UpperQuartileIntensity_FullStack_c2,Intensity,FullStack,,UpperQuartileIntensity,2,,Pr141,float +Location_CenterMassIntensity_X_FullStack_c2,Location,FullStack,,CenterMassIntensity_X,2,,Pr141,float +Location_CenterMassIntensity_Y_FullStack_c2,Location,FullStack,,CenterMassIntensity_Y,2,,Pr141,float +Location_CenterMassIntensity_Z_FullStack_c2,Location,FullStack,,CenterMassIntensity_Z,2,,Pr141,float +Location_MaxIntensity_X_FullStack_c2,Location,FullStack,,MaxIntensity_X,2,,Pr141,float +Location_MaxIntensity_Y_FullStack_c2,Location,FullStack,,MaxIntensity_Y,2,,Pr141,float +Location_MaxIntensity_Z_FullStack_c2,Location,FullStack,,MaxIntensity_Z,2,,Pr141,float +Intensity_IntegratedIntensity_FullStack_c3,Intensity,FullStack,,IntegratedIntensity,3,,Sm147,float +Intensity_MeanIntensity_FullStack_c3,Intensity,FullStack,,MeanIntensity,3,,Sm147,float +Intensity_StdIntensity_FullStack_c3,Intensity,FullStack,,StdIntensity,3,,Sm147,float +Intensity_MinIntensity_FullStack_c3,Intensity,FullStack,,MinIntensity,3,,Sm147,float +Intensity_MaxIntensity_FullStack_c3,Intensity,FullStack,,MaxIntensity,3,,Sm147,float +Intensity_IntegratedIntensityEdge_FullStack_c3,Intensity,FullStack,,IntegratedIntensityEdge,3,,Sm147,float +Intensity_MeanIntensityEdge_FullStack_c3,Intensity,FullStack,,MeanIntensityEdge,3,,Sm147,float +Intensity_StdIntensityEdge_FullStack_c3,Intensity,FullStack,,StdIntensityEdge,3,,Sm147,float +Intensity_MinIntensityEdge_FullStack_c3,Intensity,FullStack,,MinIntensityEdge,3,,Sm147,float +Intensity_MaxIntensityEdge_FullStack_c3,Intensity,FullStack,,MaxIntensityEdge,3,,Sm147,float +Intensity_MassDisplacement_FullStack_c3,Intensity,FullStack,,MassDisplacement,3,,Sm147,float +Intensity_LowerQuartileIntensity_FullStack_c3,Intensity,FullStack,,LowerQuartileIntensity,3,,Sm147,float +Intensity_MedianIntensity_FullStack_c3,Intensity,FullStack,,MedianIntensity,3,,Sm147,float +Intensity_MADIntensity_FullStack_c3,Intensity,FullStack,,MADIntensity,3,,Sm147,float +Intensity_UpperQuartileIntensity_FullStack_c3,Intensity,FullStack,,UpperQuartileIntensity,3,,Sm147,float +Location_CenterMassIntensity_X_FullStack_c3,Location,FullStack,,CenterMassIntensity_X,3,,Sm147,float +Location_CenterMassIntensity_Y_FullStack_c3,Location,FullStack,,CenterMassIntensity_Y,3,,Sm147,float +Location_CenterMassIntensity_Z_FullStack_c3,Location,FullStack,,CenterMassIntensity_Z,3,,Sm147,float +Location_MaxIntensity_X_FullStack_c3,Location,FullStack,,MaxIntensity_X,3,,Sm147,float +Location_MaxIntensity_Y_FullStack_c3,Location,FullStack,,MaxIntensity_Y,3,,Sm147,float +Location_MaxIntensity_Z_FullStack_c3,Location,FullStack,,MaxIntensity_Z,3,,Sm147,float Intensity_IntegratedIntensity_FullStack_c4,Intensity,FullStack,,IntegratedIntensity,4,,Eu153,float Intensity_MeanIntensity_FullStack_c4,Intensity,FullStack,,MeanIntensity,4,,Eu153,float Intensity_StdIntensity_FullStack_c4,Intensity,FullStack,,StdIntensity,4,,Eu153,float @@ -94,27 +94,27 @@ Location_CenterMassIntensity_Z_FullStack_c4,Location,FullStack,,CenterMassIntens Location_MaxIntensity_X_FullStack_c4,Location,FullStack,,MaxIntensity_X,4,,Eu153,float Location_MaxIntensity_Y_FullStack_c4,Location,FullStack,,MaxIntensity_Y,4,,Eu153,float Location_MaxIntensity_Z_FullStack_c4,Location,FullStack,,MaxIntensity_Z,4,,Eu153,float -Intensity_IntegratedIntensity_FullStack_c5,Intensity,FullStack,,IntegratedIntensity,5,,Ag107,float -Intensity_MeanIntensity_FullStack_c5,Intensity,FullStack,,MeanIntensity,5,,Ag107,float -Intensity_StdIntensity_FullStack_c5,Intensity,FullStack,,StdIntensity,5,,Ag107,float -Intensity_MinIntensity_FullStack_c5,Intensity,FullStack,,MinIntensity,5,,Ag107,float -Intensity_MaxIntensity_FullStack_c5,Intensity,FullStack,,MaxIntensity,5,,Ag107,float -Intensity_IntegratedIntensityEdge_FullStack_c5,Intensity,FullStack,,IntegratedIntensityEdge,5,,Ag107,float -Intensity_MeanIntensityEdge_FullStack_c5,Intensity,FullStack,,MeanIntensityEdge,5,,Ag107,float -Intensity_StdIntensityEdge_FullStack_c5,Intensity,FullStack,,StdIntensityEdge,5,,Ag107,float -Intensity_MinIntensityEdge_FullStack_c5,Intensity,FullStack,,MinIntensityEdge,5,,Ag107,float -Intensity_MaxIntensityEdge_FullStack_c5,Intensity,FullStack,,MaxIntensityEdge,5,,Ag107,float -Intensity_MassDisplacement_FullStack_c5,Intensity,FullStack,,MassDisplacement,5,,Ag107,float -Intensity_LowerQuartileIntensity_FullStack_c5,Intensity,FullStack,,LowerQuartileIntensity,5,,Ag107,float -Intensity_MedianIntensity_FullStack_c5,Intensity,FullStack,,MedianIntensity,5,,Ag107,float -Intensity_MADIntensity_FullStack_c5,Intensity,FullStack,,MADIntensity,5,,Ag107,float -Intensity_UpperQuartileIntensity_FullStack_c5,Intensity,FullStack,,UpperQuartileIntensity,5,,Ag107,float -Location_CenterMassIntensity_X_FullStack_c5,Location,FullStack,,CenterMassIntensity_X,5,,Ag107,float -Location_CenterMassIntensity_Y_FullStack_c5,Location,FullStack,,CenterMassIntensity_Y,5,,Ag107,float -Location_CenterMassIntensity_Z_FullStack_c5,Location,FullStack,,CenterMassIntensity_Z,5,,Ag107,float -Location_MaxIntensity_X_FullStack_c5,Location,FullStack,,MaxIntensity_X,5,,Ag107,float -Location_MaxIntensity_Y_FullStack_c5,Location,FullStack,,MaxIntensity_Y,5,,Ag107,float -Location_MaxIntensity_Z_FullStack_c5,Location,FullStack,,MaxIntensity_Z,5,,Ag107,float +Intensity_IntegratedIntensity_FullStack_c5,Intensity,FullStack,,IntegratedIntensity,5,,Yb172,float +Intensity_MeanIntensity_FullStack_c5,Intensity,FullStack,,MeanIntensity,5,,Yb172,float +Intensity_StdIntensity_FullStack_c5,Intensity,FullStack,,StdIntensity,5,,Yb172,float +Intensity_MinIntensity_FullStack_c5,Intensity,FullStack,,MinIntensity,5,,Yb172,float +Intensity_MaxIntensity_FullStack_c5,Intensity,FullStack,,MaxIntensity,5,,Yb172,float +Intensity_IntegratedIntensityEdge_FullStack_c5,Intensity,FullStack,,IntegratedIntensityEdge,5,,Yb172,float +Intensity_MeanIntensityEdge_FullStack_c5,Intensity,FullStack,,MeanIntensityEdge,5,,Yb172,float +Intensity_StdIntensityEdge_FullStack_c5,Intensity,FullStack,,StdIntensityEdge,5,,Yb172,float +Intensity_MinIntensityEdge_FullStack_c5,Intensity,FullStack,,MinIntensityEdge,5,,Yb172,float +Intensity_MaxIntensityEdge_FullStack_c5,Intensity,FullStack,,MaxIntensityEdge,5,,Yb172,float +Intensity_MassDisplacement_FullStack_c5,Intensity,FullStack,,MassDisplacement,5,,Yb172,float +Intensity_LowerQuartileIntensity_FullStack_c5,Intensity,FullStack,,LowerQuartileIntensity,5,,Yb172,float +Intensity_MedianIntensity_FullStack_c5,Intensity,FullStack,,MedianIntensity,5,,Yb172,float +Intensity_MADIntensity_FullStack_c5,Intensity,FullStack,,MADIntensity,5,,Yb172,float +Intensity_UpperQuartileIntensity_FullStack_c5,Intensity,FullStack,,UpperQuartileIntensity,5,,Yb172,float +Location_CenterMassIntensity_X_FullStack_c5,Location,FullStack,,CenterMassIntensity_X,5,,Yb172,float +Location_CenterMassIntensity_Y_FullStack_c5,Location,FullStack,,CenterMassIntensity_Y,5,,Yb172,float +Location_CenterMassIntensity_Z_FullStack_c5,Location,FullStack,,CenterMassIntensity_Z,5,,Yb172,float +Location_MaxIntensity_X_FullStack_c5,Location,FullStack,,MaxIntensity_X,5,,Yb172,float +Location_MaxIntensity_Y_FullStack_c5,Location,FullStack,,MaxIntensity_Y,5,,Yb172,float +Location_MaxIntensity_Z_FullStack_c5,Location,FullStack,,MaxIntensity_Z,5,,Yb172,float Intensity_IntegratedIntensity_ProbabStack_c1,Intensity,ProbabStack,,IntegratedIntensity,1,,CellCenter,float Intensity_MeanIntensity_ProbabStack_c1,Intensity,ProbabStack,,MeanIntensity,1,,CellCenter,float Intensity_StdIntensity_ProbabStack_c1,Intensity,ProbabStack,,StdIntensity,1,,CellCenter,float diff --git a/inst/extdata/mockData/steinbock/cells.csv b/inst/extdata/mockData/steinbock/cells.csv deleted file mode 100644 index 339c3ef..0000000 --- a/inst/extdata/mockData/steinbock/cells.csv +++ /dev/null @@ -1,219 +0,0 @@ -Image,Object,Ag107,Cytokeratin 5,Laminin,YBX1,H3K27Ac,area,centroid-0,centroid-1,major_axis_length,minor_axis_length,eccentricity -20210305_NE_mockData1_1.tiff,1,0.0654535807096041,0.0461538461538461,0.0769230769230769,0.0969650745391845,0.7501489602602445,65,4.523076923076923,34.01538461538462,13.001221954602691,7.025376857852489,0.8414321310455248 -20210305_NE_mockData1_1.tiff,2,0.0843829925482471,0.0581862640877564,0.0042392027874787,0.0552367692192395,0.6582037334640821,96,7.229166666666667,27.697916666666668,14.825415705000772,10.347626231090922,0.7161315464970319 -20210305_NE_mockData1_1.tiff,3,0.1242216260482867,0.0982229883472124,0.0384514760226011,0.0429215508823593,0.7953856304908792,192,19.135416666666668,37.6875,17.39292062282302,14.909630313896672,0.5149435727593397 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-20210305_NE_mockData1_1.tiff,8,0.2909258054883292,0.079393287722984,0.0643289986621128,0.0112359550561797,0.5037659781702449,89,46.52808988764045,53.24719101123596,13.10002456503396,9.134769904631176,0.716770283638874 -20210305_NE_mockData1_2.tiff,1,13.207235176033445,14.885831658707724,0.8050788482030232,7.165068136321174,2.5474712434742184,180,6.361111111111111,14.205555555555556,18.470450031922027,12.743277349001712,0.7238781675065956 -20210305_NE_mockData1_2.tiff,2,16.297462437789477,8.230757537936665,0.8875840473237462,3.371872373900489,1.3351036871915087,191,5.675392670157068,56.27225130890052,21.043601180655628,14.016882988743976,0.7458734706625134 -20210305_NE_mockData1_2.tiff,3,20.39741694242105,17.052689667405755,0.6583767704580022,4.783030694928662,3.224067460531476,87,11.494252873563218,26.17241379310345,14.871409927947424,7.642708357526635,0.8578383833893857 -20210305_NE_mockData1_2.tiff,4,14.87367583272305,0.3035827938546526,0.3827512365706423,3.140782948504103,1.9394026011862653,188,13.76063829787234,38.29255319148936,20.14354902694891,13.14866915329968,0.7575747765960211 -20210305_NE_mockData1_2.tiff,5,13.668032753936068,26.293815677928613,2.22257032352764,4.854137085410705,2.755699742569153,229,18.91703056768559,11.558951965065502,18.96163054783513,17.77474258083928,0.3482389316061158 -20210305_NE_mockData1_2.tiff,6,11.991887595042709,3.7350179617069967,1.4230037838959495,2.861593961223098,2.0478972605437287,242,19.776859504132236,51.21487603305785,20.693783540322627,15.57229499298446,0.6585799424036017 -20210305_NE_mockData1_2.tiff,7,15.564855350766862,12.033891393173308,0.8484711221286229,7.114129689761571,5.16589221840813,105,19.476190476190474,27.51428571428572,12.95033518821011,11.244906023774885,0.4960218543593225 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-28,0.43122992531894005,0.15773904486878276,0.5643250550309272,7.0494716755331375,14.14149006098917 -29,0.3167372012138367,0.06569276094436645,0.47177360534667967,3.6677976965904238,10.659761519432069 -30,0.2980427796813263,0.058253108769997786,0.36472709220031213,4.993821060520479,9.54334298769633 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_001.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_001.csv new file mode 100644 index 0000000..1248b12 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_001.csv @@ -0,0 +1,51 @@ +Object,Neighbor,Distance +1,3, +3,1, +3,5, +3,6, +3,7, +5,3, +5,7, +5,9, +6,3, +6,7, +6,8, +7,3, +7,5, +7,6, +7,8, +7,9, +7,11, +8,6, +8,7, +8,11, +8,12, +9,5, +9,7, +9,11, +10,13, +10,14, +11,7, +11,8, +11,9, +11,12, +12,8, +12,11, +12,13, +12,15, +13,10, +13,12, +13,14, +13,15, +14,10, +14,13, +14,15, +15,12, +15,13, +15,14, +15,16, +15,17, +16,15, +16,17, +17,15, +17,16, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_002.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_002.csv new file mode 100644 index 0000000..259274e --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_002.csv @@ -0,0 +1,79 @@ +Object,Neighbor,Distance +1,4, +2,6, +2,8, +3,5, +3,7, +3,9, +4,1, +4,10, +5,3, +5,6, +5,9, +5,11, +6,2, +6,5, +6,8, +6,11, +7,3, +7,9, +7,10, +8,2, +8,6, +8,11, +8,13, +9,3, +9,5, +9,7, +9,11, +9,12, +10,4, +10,7, +10,14, +10,16, +10,18, +11,5, +11,6, +11,8, +11,9, +11,12, +11,13, +11,15, +12,9, +12,11, +12,15, +12,17, +13,8, +13,11, +13,15, +14,10, +14,16, +15,11, +15,12, +15,13, +15,17, +15,20, +16,10, +16,14, +16,17, +16,18, +16,19, +17,12, +17,15, +17,16, +17,19, +17,20, +17,21, +18,10, +18,16, +18,19, +19,16, +19,17, +19,18, +19,21, +20,15, +20,17, +20,21, +21,17, +21,19, +21,20, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_003.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_003.csv new file mode 100644 index 0000000..2f71a0a --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_003.csv @@ -0,0 +1,103 @@ +Object,Neighbor,Distance +1,5, +1,10, +2,5, +2,6, +2,8, +3,4, +3,6, +3,7, +4,3, +4,7, +5,1, +5,2, +5,8, +5,10, +6,2, +6,3, +6,7, +6,8, +6,9, +7,3, +7,4, +7,6, +7,11, +8,2, +8,5, +8,6, +8,9, +8,10, +8,12, +8,13, +9,6, +9,8, +9,13, +10,1, +10,5, +10,8, +10,12, +10,15, +11,7, +11,14, +11,17, +11,20, +12,8, +12,10, +12,13, +12,15, +12,16, +12,19, +13,8, +13,9, +13,12, +13,16, +13,18, +14,11, +14,17, +14,21, +15,10, +15,12, +15,19, +16,12, +16,13, +16,18, +16,19, +17,11, +17,14, +17,20, +17,21, +18,13, +18,16, +18,19, +18,20, +18,22, +18,23, +19,12, +19,15, +19,16, +19,18, +19,22, +20,11, +20,17, +20,18, +20,21, +20,23, +20,25, +21,14, +21,17, +21,20, +21,24, +21,25, +22,18, +22,19, +22,23, +23,18, +23,20, +23,22, +23,25, +24,21, +24,25, +25,20, +25,21, +25,23, +25,24, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_1.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_1.csv deleted file mode 100644 index 9d036e7..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_1.csv +++ /dev/null @@ -1,23 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,3,1.0 -2,1,1.0 -2,3,1.0 -3,1,1.0 -3,2,1.0 -3,4,1.0 -3,5,1.0 -3,6,2.8284271247461903 -3,7,1.0 -4,3,1.0 -4,5,1.0 -5,3,1.0 -5,4,1.0 -5,7,1.0 -6,3,2.8284271247461903 -6,7,1.0 -7,3,1.0 -7,5,1.0 -7,6,1.0 -7,8,1.0 -8,7,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_2.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_2.csv deleted file mode 100644 index 146ab91..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_2.csv +++ /dev/null @@ -1,47 +0,0 @@ -Object,Neighbor,Distance -1,3,1.0 -1,5,1.0 -2,4,3.605551275463989 -2,6,1.0 -3,1,1.0 -3,4,1.0 -3,5,1.0 -3,7,1.0 -4,2,3.605551275463989 -4,3,1.0 -4,6,1.0 -4,7,1.0 -4,9,1.0 -5,1,1.0 -5,3,1.0 -5,7,1.0 -5,8,1.0 -6,2,1.0 -6,4,1.0 -6,9,1.0 -6,10,1.0 -6,11,1.0 -7,3,1.0 -7,4,1.0 -7,5,1.0 -7,8,1.0 -7,9,1.0 -8,5,1.0 -8,7,1.0 -8,9,1.0 -8,12,1.0 -9,4,1.0 -9,6,1.0 -9,7,1.0 -9,8,1.0 -9,11,1.0 -9,12,1.0 -10,6,1.0 -10,11,1.0 -11,6,1.0 -11,9,1.0 -11,10,1.0 -11,12,1.0 -12,8,1.0 -12,9,1.0 -12,11,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_3.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_3.csv deleted file mode 100644 index cc8fe56..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData1_3.csv +++ /dev/null @@ -1,49 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,4,1.0 -1,6,1.0 -2,1,1.0 -2,3,1.0 -2,4,1.0 -2,5,2.0 -2,7,1.0 -2,8,2.8284271247461903 -3,2,1.0 -3,5,1.0 -4,1,1.0 -4,2,1.0 -4,6,1.0 -4,7,1.0 -5,2,2.0 -5,3,1.0 -5,8,1.0 -5,9,1.0 -6,1,1.0 -6,4,1.0 -6,7,1.0 -7,2,1.0 -7,4,1.0 -7,6,1.0 -7,8,1.0 -7,10,1.0 -8,2,2.8284271247461903 -8,5,1.0 -8,7,1.0 -8,9,1.0 -8,10,1.0 -8,11,1.0 -8,12,1.4142135623730951 -9,5,1.0 -9,8,1.0 -9,11,1.4142135623730951 -9,12,1.0 -10,7,1.0 -10,8,1.0 -10,11,1.0 -11,8,1.0 -11,9,1.4142135623730951 -11,10,1.0 -11,12,1.0 -12,8,1.4142135623730951 -12,9,1.0 -12,11,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv new file mode 100644 index 0000000..3f8dafc --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_001.csv @@ -0,0 +1,257 @@ +Object,Neighbor,Distance +1,3, +1,4, +1,5, +2,3, +2,6, +2,7, +3,1, +3,2, +3,5, +3,7, +4,1, +4,5, +4,8, +4,9, +5,1, +5,3, +5,4, +5,7, +5,8, +5,12, +5,13, +6,2, +6,7, +6,15, +6,17, +6,18, +7,2, +7,3, +7,5, +7,6, +7,12, +7,15, +8,4, +8,5, +8,9, +8,13, +9,4, +9,8, +9,10, +9,13, +10,9, +10,11, +10,13, +10,16, +10,19, +11,10, +12,5, +12,7, +12,13, +12,14, +12,15, +13,5, +13,8, +13,9, +13,10, +13,12, +13,14, +13,19, +13,22, 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+5,7, +5,9, +6,5, +6,7, +6,9, +7,5, +7,6, +7,9, +7,10, +7,12, +8,4, +8,11, +9,5, +9,6, +9,7, +9,12, +10,7, +10,12, +11,8, +11,14, +12,7, +12,9, +12,10, +12,15, +13,16, +14,11, +14,17, +15,12, +15,18, +15,20, +16,13, +17,14, +17,18, +17,19, +18,15, +18,17, +18,19, +18,20, +18,21, +19,17, +19,18, +19,21, +20,15, +20,18, +21,18, +21,19, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv new file mode 100644 index 0000000..8feb411 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_003.csv @@ -0,0 +1,129 @@ +Object,Neighbor,Distance +1,2, +1,6, +1,7, +2,1, +2,3, +2,6, +3,2, +3,5, +4,5, +4,8, +4,9, +5,3, +5,4, +5,8, +5,13, +6,1, +6,2, +6,7, +6,10, +6,11, +7,1, +7,6, +7,11, +8,4, +8,5, +8,9, +8,13, +8,14, +9,4, +9,8, +9,14, +10,6, +10,11, +10,12, +10,16, +11,6, +11,7, +11,10, +11,16, +11,17, +12,10, +12,13, +12,16, +12,21, +13,5, +13,8, +13,12, +13,14, 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-1,5,3.605551275463989 -2,1,1.0 -2,3,1.0 -2,4,1.0 -2,5,1.0 -3,1,1.0 -3,2,1.0 -3,4,1.0 -3,6,1.0 -4,2,1.0 -4,3,1.0 -4,5,1.0 -4,6,1.0 -4,8,2.0 -5,1,3.605551275463989 -5,2,1.0 -5,4,1.0 -5,7,1.0 -6,3,1.0 -6,4,1.0 -6,8,1.0 -7,5,1.0 -7,9,1.0 -8,4,2.0 -8,6,1.0 -8,10,1.0 -9,7,1.0 -9,8,4.0 -9,10,1.0 -9,11,1.0 -10,8,1.0 -10,9,1.0 -10,11,1.0 -10,12,1.0 -11,9,1.0 -11,10,1.0 -11,12,1.0 -12,10,1.0 -12,11,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_2.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_2.csv deleted file mode 100644 index c353aae..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_2.csv +++ /dev/null @@ -1,31 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,6,3.0 -2,1,1.0 -2,3,1.0 -2,4,1.0 -3,2,1.0 -3,4,1.0 -3,5,2.23606797749979 -3,7,1.0 -4,2,1.0 -4,3,1.0 -4,8,1.0 -5,3,2.23606797749979 -5,7,1.0 -6,1,3.0 -6,10,1.0 -7,3,1.0 -7,5,1.0 -7,9,1.0 -8,4,1.0 -8,10,1.0 -8,11,1.0 -9,7,1.0 -9,11,2.0 -10,6,1.0 -10,8,1.0 -10,11,1.0 -11,8,1.0 -11,9,2.0 -11,10,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_3.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_3.csv deleted file mode 100644 index 42ab0ab..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData2_3.csv +++ /dev/null @@ -1,50 +0,0 @@ -Object,Neighbor,Distance -1,5,1.0 -1,6,1.0 -1,7,1.0 -2,3,1.0 -2,4,1.0 -3,2,1.0 -3,4,1.0 -3,5,1.0 -3,8,1.0 -3,10,3.1622776601683795 -4,2,1.0 -4,3,1.0 -4,8,1.0 -4,10,1.0 -5,1,1.0 -5,3,1.0 -5,7,1.0 -5,8,1.0 -6,1,1.0 -6,7,1.0 -6,9,1.0 -7,1,1.0 -7,5,1.0 -7,6,1.0 -7,8,1.0 -7,9,1.0 -7,12,1.0 -8,3,1.0 -8,4,1.0 -8,5,1.0 -8,7,1.0 -8,10,1.0 -8,11,1.0 -8,12,1.0 -9,6,1.0 -9,7,1.0 -9,12,1.0 -10,3,3.1622776601683795 -10,4,1.0 -10,8,1.0 -10,11,1.0 -11,8,1.0 -11,10,1.0 -11,12,1.0 -12,5,4.0 -12,7,1.0 -12,8,1.0 -12,9,1.0 -12,11,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv new file mode 100644 index 0000000..3bca874 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_001.csv @@ -0,0 +1,81 @@ +Object,Neighbor,Distance +1,2, +1,3, +1,4, +2,1, +2,3, +2,5, +3,1, +3,2, +3,4, +3,5, +3,7, +4,1, +4,3, +4,6, +4,7, +4,8, +5,2, +5,3, +5,7, +5,9, +5,11, +6,4, +6,8, +6,10, +7,3, +7,4, +7,5, +7,8, +7,11, +7,13, +8,4, +8,6, +8,7, +8,10, +8,13, +9,5, +9,11, +9,14, +9,15, +10,6, +10,8, +10,12, +10,13, +11,5, +11,7, +11,9, +11,13, +11,14, +12,10, +12,13, +13,7, +13,8, +13,10, +13,11, +13,12, +13,17, +14,9, +14,11, +14,15, +14,16, +14,20, +15,9, +15,14, +15,16, +15,18, +16,14, +16,15, +16,18, +16,20, +17,13, +17,19, +18,15, +18,16, +18,20, +19,17, +19,20, +20,14, +20,16, +20,18, +20,19, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv new file mode 100644 index 0000000..940bf78 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_002.csv @@ -0,0 +1,105 @@ +Object,Neighbor,Distance +1,2, +1,3, +1,4, +2,1, +2,4, +2,5, +2,7, +3,1, +3,4, +3,6, +3,8, +4,1, +4,2, +4,3, +4,7, +4,8, +4,9, +5,2, +5,7, +5,12, +6,3, +6,8, +6,10, +6,13, +7,2, +7,4, +7,5, +7,9, +7,12, +8,3, +8,4, +8,6, +8,9, +8,13, +9,4, +9,7, +9,8, +9,13, +9,15, +10,6, +10,11, +10,13, +10,16, +10,19, +11,10, +11,14, +11,16, +11,17, +12,5, +12,7, +12,15, +13,6, +13,8, +13,9, +13,10, +13,15, +13,19, +13,21, +14,11, +14,17, +14,18, +15,9, +15,12, +15,13, +15,21, +16,10, +16,11, +16,17, +16,19, +17,11, +17,14, +17,16, +17,18, +17,19, +17,20, +18,14, +18,17, +18,20, +18,23, +19,10, +19,13, +19,16, +19,17, +19,20, +19,22, +20,17, +20,18, +20,19, +20,22, +20,23, +20,24, +21,13, +21,15, +22,19, +22,20, +22,24, +23,18, +23,20, +23,24, +24,20, +24,22, +24,23, +25,26, +26,25, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv new file mode 100644 index 0000000..a114c04 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_003.csv @@ -0,0 +1,79 @@ +Object,Neighbor,Distance +1,3, +1,4, +2,3, +2,7, +3,1, +3,2, +3,4, +3,7, +4,1, +4,3, +4,6, +4,7, +4,10, +5,8, +5,9, +5,14, +6,4, +6,10, +6,11, +7,2, +7,3, +7,4, +7,10, +7,12, +8,5, +8,13, +8,16, +9,5, +9,14, +9,17, +10,4, +10,6, +10,7, +10,11, +10,12, +10,15, +11,6, +11,10, +12,7, +12,10, +12,15, +12,18, +13,8, +13,16, +13,19, +14,5, +14,9, +14,16, +14,17, +14,21, +15,10, +15,12, +15,18, +16,8, +16,13, +16,14, +16,19, +16,20, +16,21, +17,9, +17,14, +17,21, +17,22, +18,12, +18,15, +19,13, +19,16, +19,20, +20,16, +20,19, +20,21, +21,14, +21,16, +21,17, +21,20, +21,22, +22,17, +22,21, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_1.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_1.csv deleted file mode 100644 index fa6b6e0..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_1.csv +++ /dev/null @@ -1,52 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,6,1.0 -2,1,1.0 -2,3,1.0 -2,4,1.0 -2,6,1.0 -2,7,1.0 -3,2,1.0 -3,4,1.0 -3,5,1.0 -4,2,1.0 -4,3,1.0 -4,5,1.0 -4,7,1.0 -4,8,2.0 -5,3,1.0 -5,4,1.0 -5,7,2.23606797749979 -5,8,1.0 -5,10,3.0 -6,1,1.0 -6,2,1.0 -6,4,4.0 -6,7,1.0 -7,2,1.0 -7,4,1.0 -7,5,2.23606797749979 -7,6,1.0 -7,8,3.605551275463989 -7,9,1.0 -7,11,1.0 -8,4,2.0 -8,5,1.0 -8,7,3.605551275463989 -8,10,1.0 -8,12,2.23606797749979 -8,13,1.0 -9,7,1.0 -9,11,1.0 -10,5,3.0 -10,8,1.0 -10,13,1.0 -11,7,1.0 -11,9,1.0 -11,12,1.0 -12,8,2.23606797749979 -12,11,1.0 -12,13,1.0 -13,8,1.0 -13,10,1.0 -13,12,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_2.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_2.csv deleted file mode 100644 index 6ef2432..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_2.csv +++ /dev/null @@ -1,50 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,3,1.0 -1,5,1.0 -2,1,1.0 -2,3,1.0 -2,4,1.0 -3,1,1.0 -3,2,1.0 -3,4,1.0 -3,5,1.0 -3,6,1.0 -3,7,1.0 -4,2,1.0 -4,3,1.0 -4,6,1.0 -4,10,2.8284271247461903 -5,1,1.0 -5,3,1.0 -5,6,4.0 -5,7,1.0 -5,8,1.0 -5,9,1.0 -6,3,1.0 -6,4,1.0 -6,7,1.0 -6,10,1.0 -7,3,1.0 -7,5,1.0 -7,6,1.0 -7,8,1.0 -7,10,1.0 -7,11,2.23606797749979 -8,5,1.0 -8,7,1.0 -8,9,1.0 -8,10,1.0 -8,11,1.0 -9,5,1.0 -9,8,1.0 -9,11,1.0 -10,4,2.8284271247461903 -10,6,1.0 -10,7,1.0 -10,8,1.0 -10,11,1.0 -11,7,2.23606797749979 -11,8,1.0 -11,9,1.0 -11,10,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_3.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_3.csv deleted file mode 100644 index 3e4196a..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData3_3.csv +++ /dev/null @@ -1,27 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,3,1.0 -2,1,1.0 -2,3,1.0 -2,5,1.0 -3,1,1.0 -3,2,1.0 -3,5,1.0 -4,6,1.0 -4,8,1.0 -5,2,1.0 -5,3,1.0 -6,4,1.0 -6,7,1.0 -6,8,1.0 -6,9,2.23606797749979 -7,6,1.0 -7,8,1.0 -7,9,1.0 -8,4,1.0 -8,6,1.0 -8,7,1.0 -8,9,1.0 -9,6,2.23606797749979 -9,7,1.0 -9,8,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_001.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_001.csv new file mode 100644 index 0000000..21493d1 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_001.csv @@ -0,0 +1,37 @@ +Object,Neighbor,Distance +1,2, +1,3, +1,4, +1,5, +2,1, +2,4, +2,6, +3,1, +3,5, +3,7, +4,1, +4,2, +4,5, +4,6, +4,8, +5,1, +5,3, +5,4, +5,7, +5,8, +6,2, +6,4, +6,8, +6,9, +7,3, +7,5, +7,8, +7,9, +8,4, +8,5, +8,6, +8,7, +8,9, +9,6, +9,7, +9,8, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_002.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_002.csv new file mode 100644 index 0000000..e7e5da5 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_002.csv @@ -0,0 +1,121 @@ +Object,Neighbor,Distance +1,2, +1,4, +1,5, +2,1, +2,3, +2,5, +2,7, +3,2, +3,6, +3,7, +3,9, +4,1, +4,5, +4,10, +4,11, +5,1, +5,2, +5,4, +5,7, +5,11, +6,3, +6,8, +6,9, +6,12, +7,2, +7,3, +7,5, +7,9, +7,11, +7,13, +7,14, +8,6, +8,12, +9,3, +9,6, +9,7, +9,12, +9,14, +10,4, +10,11, +10,15, +10,20, +11,4, +11,5, +11,7, +11,10, +11,13, +11,15, +12,6, +12,8, +12,9, +12,14, +12,16, +12,18, +13,7, +13,11, +13,14, +13,15, +14,7, +14,9, +14,12, +14,13, +14,15, +14,16, +14,19, +14,21, +15,10, +15,11, +15,13, +15,14, +15,17, +15,20, +15,21, +16,12, +16,14, +16,18, +16,19, +16,22, +17,15, +17,20, +17,21, +17,24, +18,12, +18,16, +18,22, +18,23, +19,14, +19,16, +19,21, +19,22, +19,25, +20,10, +20,15, +20,17, +20,24, +21,14, +21,15, +21,17, +21,19, +21,24, +21,25, +22,16, +22,18, +22,19, +22,23, +22,25, +22,26, +23,18, +23,22, +23,26, +24,17, +24,20, +24,21, +24,25, +25,19, +25,21, +25,22, +25,24, +26,22, +26,23, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_003.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_003.csv new file mode 100644 index 0000000..8efea27 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_003.csv @@ -0,0 +1,141 @@ +Object,Neighbor,Distance +1,2, +1,3, +1,4, +2,1, +2,4, +2,6, +2,8, +3,1, +3,4, +4,1, +4,2, +4,3, +4,8, +4,10, +5,6, +5,9, +5,17, +6,2, +6,5, +6,8, +6,18, +7,11, +7,12, +7,14, +8,2, +8,4, +8,6, +8,10, +8,18, +9,5, +9,12, +9,13, +9,17, +9,21, +10,4, +10,8, +10,18, +11,7, +11,14, +11,16, +11,20, +12,7, +12,9, +12,13, +12,14, +12,15, +13,9, +13,12, +13,15, +13,21, +14,7, +14,11, +14,12, +14,15, +14,20, +14,24, +15,12, +15,13, +15,14, +15,21, +15,24, +16,11, +16,20, +16,23, +17,5, +17,9, +17,19, +17,21, +17,22, +17,25, +18,6, +18,8, +18,10, +18,19, +19,17, +19,18, +19,22, +20,11, +20,14, +20,16, +20,23, +20,24, +20,27, +21,9, +21,13, +21,15, +21,17, +21,24, +21,25, +21,26, +22,17, +22,19, +22,25, +23,16, +23,20, +23,27, +23,30, +24,14, +24,15, +24,20, +24,21, +24,26, +24,27, +24,28, +25,17, +25,21, +25,22, +25,26, +25,29, +26,21, +26,24, +26,25, +26,28, +26,29, +27,20, +27,23, +27,24, +27,28, +27,30, +27,32, +28,24, +28,26, +28,27, +28,29, +28,31, +28,32, +29,25, +29,26, +29,28, +29,31, +30,23, +30,27, +31,28, +31,29, +31,32, +32,27, +32,28, +32,31, +33,34, +34,33, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_1.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_1.csv deleted file mode 100644 index 66d92bd..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_1.csv +++ /dev/null @@ -1,27 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,3,1.0 -1,4,1.0 -1,7,2.0 -2,1,1.0 -2,4,1.0 -2,6,1.0 -3,1,1.0 -3,4,1.0 -3,5,1.0 -3,7,1.0 -4,1,1.0 -4,2,1.0 -4,3,1.0 -4,6,1.0 -4,7,1.0 -5,3,1.0 -5,7,1.0 -6,2,1.0 -6,4,1.0 -6,7,1.0 -7,1,2.0 -7,3,1.0 -7,4,1.0 -7,5,1.0 -7,6,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_2.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_2.csv deleted file mode 100644 index ce9df9a..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData4_2.csv +++ /dev/null @@ -1,71 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,3,1.0 -1,4,2.23606797749979 -1,6,1.4142135623730951 -2,1,1.0 -2,3,1.0 -2,4,1.0 -2,6,1.0 -3,1,1.0 -3,2,1.0 -3,4,1.0 -3,5,1.0 -3,7,1.0 -3,8,1.0 -4,1,2.23606797749979 -4,2,1.0 -4,3,1.0 -4,6,1.0 -4,7,1.0 -4,9,3.605551275463989 -5,3,1.0 -5,8,1.0 -6,1,1.4142135623730951 -6,2,1.0 -6,4,1.0 -6,7,1.0 -6,9,1.0 -6,10,3.605551275463989 -6,11,1.0 -7,3,1.0 -7,4,1.0 -7,6,1.0 -7,8,1.0 -7,9,1.0 -7,10,1.0 -7,12,3.605551275463989 -8,3,1.0 -8,5,1.0 -8,7,1.0 -8,10,1.0 -8,12,1.0 -9,4,3.605551275463989 -9,6,1.0 -9,7,1.0 -9,10,1.0 -9,11,1.0 -9,13,1.0 -9,14,1.4142135623730951 -10,6,3.605551275463989 -10,7,1.0 -10,8,1.0 -10,9,1.0 -10,12,1.0 -10,13,1.4142135623730951 -10,14,1.0 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file mode 100644 index 0000000..d0e9c3a --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_001.csv @@ -0,0 +1,69 @@ +Object,Neighbor,Distance +1,2, +1,3, +1,4, +1,6, +2,1, +2,4, +2,5, +2,9, +3,1, +3,6, +3,7, +4,1, +4,2, +4,6, +4,9, +5,2, +5,8, +5,9, +6,1, +6,3, +6,4, +6,7, +6,9, +6,10, +7,3, +7,6, +7,10, +7,12, +8,5, +8,9, +8,13, +8,14, +9,2, +9,4, +9,5, +9,6, +9,8, +9,10, +9,11, +9,13, +10,6, +10,7, +10,9, +10,11, +10,12, +11,9, +11,10, +11,12, +11,13, +11,15, +11,16, +12,7, +12,10, +12,11, +12,15, +13,8, +13,9, +13,11, +13,14, +14,8, +14,13, +14,16, +15,11, +15,12, +15,16, +16,11, +16,14, +16,15, diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_002.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_002.csv new file mode 100644 index 0000000..ad75730 --- /dev/null +++ b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_002.csv @@ -0,0 +1,201 @@ +Object,Neighbor,Distance +1,2, +1,3, +1,4, 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-10,5,1.0 -10,6,3.0 -10,7,1.0 -10,8,1.0 -10,12,1.0 -11,7,3.605551275463989 -11,9,1.0 -11,12,1.0 -12,6,3.1622776601683795 -12,7,1.0 -12,8,2.23606797749979 -12,9,1.0 -12,10,1.0 -12,11,1.0 diff --git a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_2.csv b/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_2.csv deleted file mode 100644 index 99ad229..0000000 --- a/inst/extdata/mockData/steinbock/neighbors/20210305_NE_mockData5_2.csv +++ /dev/null @@ -1,164 +0,0 @@ -Object,Neighbor,Distance -1,2,1.0 -1,3,2.23606797749979 -1,4,1.0 -1,5,1.0 -2,1,1.0 -2,3,1.0 -2,5,1.0 -2,7,1.0 -2,8,2.8284271247461903 -3,1,2.23606797749979 -3,2,1.0 -3,6,1.0 -3,7,1.0 -3,8,1.0 -3,9,1.0 -3,10,1.0 -4,1,1.0 -4,5,1.0 -4,11,1.0 -4,12,2.8284271247461903 -5,1,1.0 -5,2,1.0 -5,4,1.0 -5,7,1.0 -5,11,1.0 -5,12,1.0 -6,3,1.0 -6,7,3.605551275463989 -6,8,1.0 -6,9,1.0 -6,13,3.1622776601683795 -7,2,1.0 -7,3,1.0 -7,5,1.0 -7,6,3.605551275463989 -7,8,1.0 -7,12,1.0 -7,13,1.4142135623730951 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-21,51,44.8235294117647,51.588235294117645,9.588384705175542,7.445806966025477,0.630062465868717 -22,193,41.626943005181346,20.259067357512954,18.723469417296112,14.215094728491406,0.6508426542535845 -23,160,42.8625,34.4,21.947823059145623,9.509498565352194,0.9012605516394727 -24,121,49.570247933884296,14.62809917355372,19.478633568692487,8.761863568257516,0.8931196325838626 -25,174,51.55172413793103,58.01149425287356,24.017703275617194,10.745828278344101,0.8943275525562451 -26,162,53.598765432098766,28.962962962962962,17.665772207043837,12.455917392677373,0.7091201867118193 -27,214,54.6588785046729,67.17289719626169,24.09567195916124,11.655994771509558,0.8752127984597066 -28,117,54.52136752136752,45.085470085470085,14.118677446397097,11.366104544235725,0.5932201030042233 -29,70,57.94285714285714,37.371428571428574,11.829334186407838,8.055617614761912,0.7322959120387358 -30,89,60.19101123595506,21.168539325842698,13.041610913839078,8.854728788269489,0.7341755021928841 diff --git a/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_3.csv b/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_3.csv deleted file mode 100644 index e6f2869..0000000 --- a/inst/extdata/mockData/steinbock/regionprops/20210305_NE_mockData5_3.csv +++ /dev/null @@ -1,31 +0,0 @@ -Object,area,centroid-0,centroid-1,major_axis_length,minor_axis_length,eccentricity -1,51,10.470588235294118,29.019607843137255,8.897123703079927,7.868877729201914,0.4666740256377402 -2,165,13.218181818181819,37.981818181818184,18.70125724900904,11.802117375774815,0.775712187639427 -3,111,13.216216216216216,49.2972972972973,17.089648626038397,8.772281279550542,0.858203483886608 -4,104,19.298076923076923,28.721153846153847,13.584466977882586,10.87819093378611,0.5989564764547731 -5,98,18.73469387755102,20.081632653061224,13.633449475645289,10.598339830611351,0.629034088772814 -6,110,22.51818181818182,44.95454545454545,13.001297236709247,11.146165886276295,0.5147974664181929 -7,140,25.085714285714285,56.207142857142856,15.185302480619578,12.404017486144511,0.5768591652007239 -8,110,27.645454545454545,19.427272727272726,16.457590688973465,8.878832081272682,0.8419870828132374 -9,114,34.35087719298246,54.3421052631579,17.80333211073713,8.454564119989445,0.8800469890806012 -10,153,35.63398692810458,44.150326797385624,19.0458859533247,10.862368014449682,0.8214182920035773 -11,164,37.176829268292686,18.23780487804878,17.782118369923833,12.43327278824274,0.7149252627484994 -12,90,36.27777777777778,31.633333333333333,12.869446093876807,9.810001155397375,0.6472584046376308 -13,109,41.77981651376147,70.28440366972477,19.59918986045094,7.14746815622711,0.9311321994558601 -14,75,45.693333333333335,43.38666666666666,12.088069131467702,8.989347164874403,0.668564106928393 -15,110,45.38181818181818,35.46363636363636,14.144176870363804,10.623618447794914,0.6601943060487855 -16,117,45.64102564102564,23.735042735042736,13.6725357292778,11.557207073573382,0.534313652291959 -17,132,46.06060606060606,54.166666666666664,15.863563646427249,11.365626591232253,0.6976270223198264 -18,102,49.15686274509804,62.61764705882353,17.36825945598008,7.6030814031098775,0.8990932069546752 -19,83,50.16867469879518,70.27710843373494,13.514400676182486,9.36360670653288,0.7210707778458544 -20,51,51.470588235294116,30.215686274509803,10.608868703050506,6.4979340310210025,0.7904704452337845 -21,97,53.75257731958763,79.4639175257732,16.310830776460726,7.867968870442277,0.8759637401487904 -22,176,56.49431818181818,50.38068181818182,19.893676648669295,12.113653302795928,0.7932318045438445 -23,116,58.98275862068966,71.6896551724138,15.755441765377332,10.17838819695489,0.7633173830150044 -24,26,62.80769230769231,53.46153846153846,8.447039950456858,4.336053762262635,0.8581959229958517 -25,71,64.66197183098592,58.23943661971831,13.399133185985027,7.294566512423287,0.838821952964843 -26,106,67.78301886792453,73.21698113207547,13.791386632574282,10.79432646678499,0.6224166497784818 -27,88,67.54545454545455,47.01136363636363,12.129733257195404,9.62562356216611,0.6084971237217418 -28,73,66.94520547945206,63.794520547945204,13.708828445261855,7.226420073035162,0.8497807955620025 -29,50,74.26,65.74,10.319944203117416,6.41058122517321,0.7836649785851371 -30,87,73.65517241379311,54.839080459770116,12.823939065995026,9.048394685819856,0.708624079978646 diff --git a/inst/extdata/mockData/steinbock/steinbock.sh b/inst/extdata/mockData/steinbock/steinbock.sh index 2cef2d1..c3ea0ee 100644 --- a/inst/extdata/mockData/steinbock/steinbock.sh +++ b/inst/extdata/mockData/steinbock/steinbock.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash base_dir=$(cd -- "$(dirname "${BASH_SOURCE[0]}")" && pwd -P) -steinbock="docker run -v ${base_dir}:/data -v /tmp/.X11-unix:/tmp/.X11-unix -v ${HOME}/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY ghcr.io/bodenmillergroup/steinbock:0.8.0" +steinbock="docker run -v ${base_dir}:/data -v /tmp/.X11-unix:/tmp/.X11-unix -v ${HOME}/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY ghcr.io/bodenmillergroup/steinbock:0.16.1" cd "${base_dir}" @@ -17,16 +17,24 @@ $steinbock classify ilastik fix --no-backup $steinbock classify ilastik run $steinbock segment cellprofiler prepare -$steinbock segment cellprofiler run +$steinbock segment cellprofiler run -o masks_ilastik -$steinbock measure intensities -$steinbock measure regionprops -$steinbock measure neighbors --type borders --dmax 4 -$steinbock measure cellprofiler prepare +$steinbock measure intensities --masks masks_ilastik -o intensities_ilastik +$steinbock measure regionprops --masks masks_ilastik -o regionprops_ilastik +$steinbock measure neighbors --type expansion --dmax 4 --masks masks_ilastik -o neighbors_ilastik +$steinbock measure cellprofiler prepare --masks masks_ilastik $steinbock measure cellprofiler run +# deep learning-based segmentation +$steinbock segment deepcell --minmax -o masks_deepcell + +# measurement +$steinbock measure intensities --masks masks_deepcell -o intensities_deepcell +$steinbock measure regionprops --masks masks_deepcell -o regionprops_deepcell +$steinbock measure neighbors --masks masks_deepcell --type expansion --dmax 4 -o neighbors_deepcell + $steinbock export ome -$steinbock export csv intensities regionprops -o cells.csv -$steinbock export fcs intensities regionprops -o cells.fcs -$steinbock export anndata --x intensities --obs regionprops -$steinbock export graphs --data intensities --data regionprops +$steinbock export csv intensities_deepcell regionprops_deepcell -o cells.csv +$steinbock export fcs intensities_deepcell regionprops_deepcell -o cells.fcs +$steinbock export anndata --intensities intensities_deepcell --data regionprops_deepcell --neighbors neighbors_deepcell -o cells.h5ad +$steinbock export graphs --data intensities_deepcell --data regionprops_deepcell --neighbors neighbors_deepcell diff --git a/inst/scripts/download_TestData_cpout.Rmd b/inst/scripts/download_TestData_cpout.Rmd index 17e3ec6..2e4140d 100644 --- a/inst/scripts/download_TestData_cpout.Rmd +++ b/inst/scripts/download_TestData_cpout.Rmd @@ -20,7 +20,7 @@ Here, we will first download the output of the standard [ImcSegmentationPipeline For this, we an use the automatically generated Github assets. ```{r download-cpout} -cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.9/210308_ImcTestData_analysis_cpout.tar.gz" +cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.10/210308_ImcTestData_analysis_cpout.tar.gz" download.file(cur_url, "210308_ImcTestData_analysis_cpout.tar.gz") untar("210308_ImcTestData_analysis_cpout.tar.gz") diff --git a/inst/scripts/download_TestData_steinbock.Rmd b/inst/scripts/download_TestData_steinbock.Rmd index 7e08d10..b621e59 100644 --- a/inst/scripts/download_TestData_steinbock.Rmd +++ b/inst/scripts/download_TestData_steinbock.Rmd @@ -20,7 +20,7 @@ Here, we will first download the output of the [steinbock](https://github.com/Bo For this, we an use the automatically generated Github assets. ```{r download-cpout} -cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.7/210308_ImcTestData_steinbock.tar.gz" +cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.10/210308_ImcTestData_steinbock.tar.gz" download.file(cur_url, "210308_ImcTestData_steinbock.tar.gz") untar("210308_ImcTestData_steinbock.tar.gz") @@ -32,13 +32,13 @@ unlink("210308_ImcTestData_steinbock.tar.gz") For reading in the single-cell features, we will only need to copy the .csv files and the folders containing the individual measurements. ```{r copy-files, message=FALSE} -files_of_interest <- c("cells.csv", "panel.csv", "steinbock.sh", "images.csv") +files_of_interest <- c("panel.csv", "steinbock.sh", "images.csv") folders_of_interest <- c("neighbors", "intensities", "regionprops") lapply(folders_of_interest, function(x){ dir.create(paste0("../extdata/mockData/steinbock/", x)) - file.copy(list.files(paste0("datasets/210308_ImcTestData/steinbock/", x), + file.copy(list.files(paste0("datasets/210308_ImcTestData/steinbock/", x, "_deepcell"), full.names = TRUE), paste0("../extdata/mockData/steinbock/", x), overwrite = TRUE) From 5c6522c76a393e2b465b08b3ffce293c7266916a Mon Sep 17 00:00:00 2001 From: nilseling Date: Tue, 26 Sep 2023 18:12:58 +0200 Subject: [PATCH 2/4] Adjusted steinbock unit tests --- DESCRIPTION | 2 +- NEWS | 4 + tests/testthat/test_read_steinbock.R | 353 +++++++++++++-------------- 3 files changed, 170 insertions(+), 189 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 58875ad..abe0c9a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: imcRtools -Version: 1.7.5 +Version: 1.7.6 Title: Methods for imaging mass cytometry data analysis Description: This R package supports the handling and analysis of imaging mass cytometry diff --git a/NEWS b/NEWS index 682f13e..8b71d86 100644 --- a/NEWS +++ b/NEWS @@ -201,3 +201,7 @@ Changes in version 1.7.5 (2023-09-14) + Stop allowing Object numbers to be different between intensities and regionprops + Stop allowing missing files in regionprops and neighbors +Changes in version 1.7.6 (2023-09-26) + ++ Updated example data in "inst" to newest version + diff --git a/tests/testthat/test_read_steinbock.R b/tests/testthat/test_read_steinbock.R index bd8435c..91ebf99 100644 --- a/tests/testthat/test_read_steinbock.R +++ b/tests/testthat/test_read_steinbock.R @@ -9,12 +9,13 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 218)) + expect_equal(dim(cur_spe), c(5, 404)) expect_equal(names(rowData(cur_spe)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", + "Tube.Number")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area", - "major_axis_length", - "minor_axis_length", "eccentricity", + "axis_major_length", + "axis_minor_length", "eccentricity", "width_px", "height_px")) expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y")) @@ -23,19 +24,17 @@ test_that("read_steinbock function works", { cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_spe), t(cur_counts[,-1])) - expect_equal(counts(cur_spe)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) + expect_equal(counts(cur_spe)[1:10], c(0.0909090909090909, 0.181818181818182, 0.0909090909090909, + 0.0909090909090909, 0.938306353308938, 0.181163804871695, 0, + 0.142857142857143, 0.501448290688651, 1.00346943310329)) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_morph <- do.call("rbind", cur_morph) expect_equal(cur_spe$area, cur_morph$area) - expect_equal(cur_spe$major_axis_length, cur_morph$major_axis_length) - expect_equal(cur_spe$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length) + expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_spe$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`) expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`) @@ -48,23 +47,28 @@ test_that("read_steinbock function works", { expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik) expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) - expect_equal(colPairNames(cur_spe), "neighborhood") + cur_images <- readr::read_csv(file.path(path, "images.csv"), show_col_types = FALSE) + cur_images <- cur_images[order(cur_images$image, decreasing = FALSE),] - expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData1_3.csv"), show_col_types = FALSE) + cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")]) - expect_equal(cur_test$Object + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData1_3")]) - expect_equal(cur_test$Neighbor + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData1_3")]) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(cur_images$width_px, cur_test$width_px) + expect_equal(cur_images$height_px, cur_test$height_px) + + expect_equal(colPairNames(cur_spe), "neighborhood") expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData2_1.csv"), show_col_types = FALSE) - expect_equal(cur_test$Object + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData2_1")]) - expect_equal(cur_test$Neighbor + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData2_1")]) + for (i in unique(cur_spe$sample_id)) { + cur_dat <- cur_spe[,cur_spe$sample_id == i] + + cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE) + + expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood"))) + expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood"))) + } # SingleCellExperiment cur_sce <- read_steinbock(path, return_as = "sce") @@ -74,13 +78,13 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 218)) + expect_equal(dim(cur_sce), c(5, 404)) expect_equal(names(rowData(cur_sce)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "area", - "major_axis_length", - "minor_axis_length", "eccentricity", + "axis_major_length", + "axis_minor_length", "eccentricity", "width_px", "height_px")) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE) @@ -88,19 +92,17 @@ test_that("read_steinbock function works", { cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_sce), t(cur_counts[,-1])) - expect_equal(counts(cur_sce)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) + expect_equal(counts(cur_sce)[1:10], c(0.0909090909090909, 0.181818181818182, 0.0909090909090909, + 0.0909090909090909, 0.938306353308938, 0.181163804871695, 0, + 0.142857142857143, 0.501448290688651, 1.00346943310329)) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_morph <- do.call("rbind", cur_morph) expect_equal(cur_sce$area, cur_morph$area) - expect_equal(cur_sce$major_axis_length, cur_morph$major_axis_length) - expect_equal(cur_sce$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length) + expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_sce$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`) expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`) @@ -116,20 +118,22 @@ test_that("read_steinbock function works", { expect_equal(colPairNames(cur_sce), "neighborhood") expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData1_3.csv"), show_col_types = FALSE) - expect_equal(cur_test$Object + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData1_3")]) - expect_equal(cur_test$Neighbor + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData1_3")]) + for (i in unique(cur_sce$sample_id)) { + cur_dat <- cur_sce[,cur_sce$sample_id == i] + + cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE) + + expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood"))) + expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood"))) + } - expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData2_1.csv"), show_col_types = FALSE) + cur_test <- unique(colData(cur_sce)[,c("sample_id", "width_px", "height_px")]) - expect_equal(cur_test$Object + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData2_1")]) - expect_equal(cur_test$Neighbor + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData2_1")]) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(cur_images$width_px, cur_test$width_px) + expect_equal(cur_images$height_px, cur_test$height_px) # Test other import settings cur_spe <- read_steinbock(path, regionprops_folder = NULL) @@ -137,9 +141,9 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 218)) + expect_equal(dim(cur_spe), c(5, 404)) expect_equal(names(rowData(cur_spe)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "width_px", "height_px")) expect_null(spatialCoordsNames(cur_spe)) @@ -149,11 +153,6 @@ test_that("read_steinbock function works", { cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_spe), t(cur_counts[,-1])) - expect_equal(counts(cur_spe)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) @@ -167,32 +166,36 @@ test_that("read_steinbock function works", { expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell) expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) - expect_equal(colPairNames(cur_sce), "neighborhood") + expect_equal(colPairNames(cur_spe), "neighborhood") expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData1_3.csv"), show_col_types = FALSE) - expect_equal(cur_test$Object + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData1_3")]) - expect_equal(cur_test$Neighbor + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData1_3")]) + for (i in unique(cur_spe$sample_id)) { + cur_dat <- cur_spe[,cur_spe$sample_id == i] + + cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE) + + expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood"))) + expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood"))) + } - expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData2_1.csv"), show_col_types = FALSE) + expect_equal(length(colPair(cur_spe)), 1674) + + cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")]) - expect_equal(cur_test$Object + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData2_1")]) - expect_equal(cur_test$Neighbor + sum(cur_spe$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData2_1")]) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(cur_images$width_px, cur_test$width_px) + expect_equal(cur_images$height_px, cur_test$height_px) cur_sce <- read_steinbock(path, return_as = "sce", regionprops_folder = NULL) expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 218)) + expect_equal(dim(cur_sce), c(5, 404)) expect_equal(names(rowData(cur_sce)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "width_px", "height_px")) @@ -201,11 +204,6 @@ test_that("read_steinbock function works", { cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_sce), t(cur_counts[,-1])) - expect_equal(counts(cur_sce)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) @@ -221,60 +219,40 @@ test_that("read_steinbock function works", { expect_equal(colPairNames(cur_sce), "neighborhood") - expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData1_3.csv"), show_col_types = FALSE) - - expect_equal(cur_test$Object + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData1_3")]) - expect_equal(cur_test$Neighbor + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData1_3")]) - - expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData2_1.csv")) - - expect_equal(cur_test$Object + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData2_1")]) - expect_equal(cur_test$Neighbor + sum(cur_sce$sample_id %in% c("20210305_NE_mockData1_1", "20210305_NE_mockData1_2", "20210305_NE_mockData1_3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData2_1")]) - + expect_equal(length(colPair(cur_sce)), 1674) cur_spe <- read_steinbock(path, graphs_folder = NULL) expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 218)) + expect_equal(dim(cur_spe), c(5, 404)) expect_equal(names(rowData(cur_spe)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area", - "major_axis_length", - "minor_axis_length", "eccentricity", + "axis_major_length", + "axis_minor_length", "eccentricity", "width_px", "height_px")) expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y")) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE) - cur_counts <- lapply(cur_files, readr::read_csv) + cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_spe), t(cur_counts[,-1])) - expect_equal(counts(cur_spe)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) - cur_morph <- lapply(cur_files, readr::read_csv) + cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_morph <- do.call("rbind", cur_morph) expect_equal(cur_spe$area, cur_morph$area) - expect_equal(cur_spe$major_axis_length, cur_morph$major_axis_length) - expect_equal(cur_spe$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length) + expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_spe$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`) expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`) - cur_panel <- readr::read_csv(file.path(path, "panel.csv")) + cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE) expect_equal(rowData(cur_spe)$name, cur_panel$name) expect_equal(rowData(cur_spe)$channel, cur_panel$channel) expect_equal(rowData(cur_spe)$keep, cur_panel$keep) @@ -291,38 +269,33 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 218)) + expect_equal(dim(cur_sce), c(5, 404)) expect_equal(names(rowData(cur_sce)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "area", - "major_axis_length", - "minor_axis_length", "eccentricity", + "axis_major_length", + "axis_minor_length", "eccentricity", "width_px", "height_px")) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE) - cur_counts <- lapply(cur_files, readr::read_csv) + cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_sce), t(cur_counts[,-1])) - expect_equal(counts(cur_sce)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) - cur_morph <- lapply(cur_files, readr::read_csv) + cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_morph <- do.call("rbind", cur_morph) expect_equal(cur_sce$area, cur_morph$area) - expect_equal(cur_sce$major_axis_length, cur_morph$major_axis_length) - expect_equal(cur_sce$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length) + expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_sce$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`) expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`) - cur_panel <- readr::read_csv(file.path(path, "panel.csv")) + cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE) expect_equal(rowData(cur_sce)$name, cur_panel$name) expect_equal(rowData(cur_sce)$channel, cur_panel$channel) expect_equal(rowData(cur_sce)$keep, cur_panel$keep) @@ -337,29 +310,29 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 218)) + expect_equal(dim(cur_spe), c(5, 404)) expect_equal(names(rowData(cur_spe)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "width_px", "height_px")) expect_null(spatialCoordsNames(cur_spe)) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE) - cur_counts <- lapply(cur_files, readr::read_csv) + cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_spe), t(cur_counts[,-1])) - expect_equal(counts(cur_spe)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) - cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) - cur_morph <- lapply(cur_files, readr::read_csv) - cur_morph <- do.call("rbind", cur_morph) + expect_equal(cur_spe$ObjectNumber, cur_counts$Object) - cur_panel <- readr::read_csv(file.path(path, "panel.csv")) + cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")]) + + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id) + expect_equal(cur_images$width_px, cur_test$width_px) + expect_equal(cur_images$height_px, cur_test$height_px) + + cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE) expect_equal(rowData(cur_spe)$name, cur_panel$name) expect_equal(rowData(cur_spe)$channel, cur_panel$channel) expect_equal(rowData(cur_spe)$keep, cur_panel$keep) @@ -376,28 +349,19 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 218)) + expect_equal(dim(cur_sce), c(5, 404)) expect_equal(names(rowData(cur_sce)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "width_px", "height_px")) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE) - cur_counts <- lapply(cur_files, readr::read_csv) + cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_sce), t(cur_counts[,-1])) - expect_equal(counts(cur_sce)[1:10], c(0.065453581, 0.046153846, 0.076923077, - 0.096965075, 0.750148960, 0.084382993, - 0.058186264, 0.004239203, 0.055236769, - 0.658203733), - tolerance = 10e-6) - cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) - cur_morph <- lapply(cur_files, readr::read_csv) - cur_morph <- do.call("rbind", cur_morph) - - cur_panel <- readr::read_csv(file.path(path, "panel.csv")) + cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE) expect_equal(rowData(cur_sce)$name, cur_panel$name) expect_equal(rowData(cur_sce)$channel, cur_panel$channel) expect_equal(rowData(cur_sce)$keep, cur_panel$keep) @@ -414,33 +378,31 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 35)) + expect_equal(dim(cur_spe), c(5, 106)) expect_equal(names(rowData(cur_spe)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area", - "major_axis_length", - "minor_axis_length", "eccentricity", + "axis_major_length", + "axis_minor_length", "eccentricity", "width_px", "height_px")) expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y")) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE, pattern = "mockData2") - cur_counts <- lapply(cur_files, readr::read_csv) + cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_spe), t(cur_counts[,-1])) - expect_equal(counts(cur_spe)[1:10], c(0.38237867, 0.04112295, 6.88474564, - 5.65280831, 2.44857732, 0.53002120, - 0.08389935, 2.76029619, 8.47630586, - 3.58901901), - tolerance = 10e-6) + expect_equal(counts(cur_spe)[1:10], c(0.399655099572807, 0.0344827586206896, 4.64201253035973, 6.50705560733532, + 3.57779644892133, 0.428760413080454, 0.0945868939161301, 1.56471130624413, + 8.0167475938797, 1.46797196567059)) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE, pattern = "mockData2") - cur_morph <- lapply(cur_files, readr::read_csv) + cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE) cur_morph <- do.call("rbind", cur_morph) expect_equal(cur_spe$area, cur_morph$area) - expect_equal(cur_spe$major_axis_length, cur_morph$major_axis_length) - expect_equal(cur_spe$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length) + expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_spe$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`) expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`) @@ -455,13 +417,23 @@ test_that("read_steinbock function works", { expect_equal(colPairNames(cur_spe), "neighborhood") - expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData2_3.csv")) + for (i in unique(cur_spe$sample_id)) { + cur_dat <- cur_spe[,cur_spe$sample_id == i] + + cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE) + + expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood"))) + expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood"))) + } + + cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")]) + + cur_images_2 <- cur_images[grepl("mockData2", cur_images$image),] - expect_equal(cur_test$Object + sum(cur_spe$sample_id %in% c("20210305_NE_mockData2_1", "20210305_NE_mockData2_2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData2_3")]) - expect_equal(cur_test$Neighbor + sum(cur_spe$sample_id %in% c("20210305_NE_mockData2_1", "20210305_NE_mockData2_2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "20210305_NE_mockData2_3")]) + expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id) + expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id) + expect_equal(cur_images_2$width_px, cur_test$width_px) + expect_equal(cur_images_2$height_px, cur_test$height_px) cur_sce <- read_steinbock(path, pattern = "mockData2", return_as = "sce") @@ -470,13 +442,13 @@ test_that("read_steinbock function works", { expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin", "YBX1", "H3K27Ac")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 35)) + expect_equal(dim(cur_sce), c(5, 106)) expect_equal(names(rowData(cur_sce)), - c("channel", "name", "keep", "ilastik", "deepcell", "Tube.Number")) + c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "area", - "major_axis_length", - "minor_axis_length", "eccentricity", + "axis_major_length", + "axis_minor_length", "eccentricity", "width_px", "height_px")) cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE, pattern = "mockData2") @@ -484,19 +456,14 @@ test_that("read_steinbock function works", { cur_counts <- do.call("rbind", cur_counts) expect_equal(counts(cur_sce), t(cur_counts[,-1])) - expect_equal(counts(cur_sce)[1:10], c(0.38237867, 0.04112295, 6.88474564, - 5.65280831, 2.44857732, 0.53002120, - 0.08389935, 2.76029619, 8.47630586, - 3.58901901), - tolerance = 10e-6) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE, pattern = "mockData2") cur_morph <- lapply(cur_files, readr::read_csv) cur_morph <- do.call("rbind", cur_morph) expect_equal(cur_sce$area, cur_morph$area) - expect_equal(cur_sce$major_axis_length, cur_morph$major_axis_length) - expect_equal(cur_sce$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length) + expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_sce$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`) expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`) @@ -512,12 +479,22 @@ test_that("read_steinbock function works", { expect_equal(colPairNames(cur_sce), "neighborhood") expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- readr::read_csv(file.path(path, "neighbors", "20210305_NE_mockData2_3.csv")) - - expect_equal(cur_test$Object + sum(cur_sce$sample_id %in% c("20210305_NE_mockData2_1", "20210305_NE_mockData2_2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData2_3")]) - expect_equal(cur_test$Neighbor + sum(cur_sce$sample_id %in% c("20210305_NE_mockData2_1", "20210305_NE_mockData2_2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "20210305_NE_mockData2_3")]) + + for (i in unique(cur_sce$sample_id)) { + cur_dat <- cur_sce[,cur_sce$sample_id == i] + + cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE) + + expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood"))) + expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood"))) + } + + cur_test <- unique(colData(cur_sce)[,c("sample_id", "width_px", "height_px")]) + + expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id) + expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id) + expect_equal(cur_images_2$width_px, cur_test$width_px) + expect_equal(cur_images_2$height_px, cur_test$height_px) cur_spe <- read_steinbock(path, panel = NULL) @@ -527,10 +504,10 @@ test_that("read_steinbock function works", { expect_equal(length(rowData(cur_sce)), 0) - cur_spe <- read_steinbock(path, extract_coords_from = c("area", "major_axis_length")) + cur_spe <- read_steinbock(path, extract_coords_from = c("area", "axis_major_length")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "centroid.0", - "centroid.1", "minor_axis_length", "eccentricity", + "centroid.1", "axis_minor_length", "eccentricity", "width_px", "height_px")) expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y")) @@ -540,15 +517,15 @@ test_that("read_steinbock function works", { expect_equal(cur_spe$`centroid.1`, cur_morph$`centroid-1`) expect_equal(cur_spe$`centroid.0`, cur_morph$`centroid-0`) - expect_equal(cur_spe$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_spe$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$area) - expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$major_axis_length) + expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$axis_major_length) - cur_sce <- read_steinbock(path, return_as = "sce", extract_coords_from = c("area", "major_axis_length")) + cur_sce <- read_steinbock(path, return_as = "sce", extract_coords_from = c("area", "axis_major_length")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "centroid.0", - "centroid.1", "minor_axis_length", "eccentricity", + "centroid.1", "axis_minor_length", "eccentricity", "width_px", "height_px")) cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE) @@ -557,10 +534,10 @@ test_that("read_steinbock function works", { expect_equal(cur_sce$`centroid.0`, cur_morph$`centroid-0`) expect_equal(cur_sce$`centroid.1`, cur_morph$`centroid-1`) - expect_equal(cur_sce$minor_axis_length, cur_morph$minor_axis_length) + expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length) expect_equal(cur_sce$eccentricity, cur_morph$eccentricity) expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$area) - expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$major_axis_length) + expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$axis_major_length) # This test doesn't make sense anymore #cur_spe <- read_steinbock(path, extract_names_from = "channel") @@ -572,15 +549,16 @@ test_that("read_steinbock function works", { cur_spe <- read_steinbock(path, image_file = NULL) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area", - "major_axis_length", "minor_axis_length", "eccentricity")) + "axis_major_length", "axis_minor_length", "eccentricity")) cur_sce <- read_steinbock(path, image_file = NULL, return_as = "sce") expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "area", - "major_axis_length", "minor_axis_length", "eccentricity")) + "axis_major_length", "axis_minor_length", "eccentricity")) cur_spe <- read_steinbock(path) cur_images_file <- readr::read_csv(file.path(path, "images.csv"), show_col_types = FALSE) + cur_images_file <- cur_images_file[order(cur_images_file$image, decreasing = FALSE),] cur_df <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")]) expect_equal(cur_images_file$image, paste0(cur_df$sample_id, ".tiff")) @@ -590,7 +568,7 @@ test_that("read_steinbock function works", { cur_spe <- read_steinbock(path, extract_imagemetadata_from = c("recovered", "acquisition_description")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area", - "major_axis_length", "minor_axis_length", + "axis_major_length", "axis_minor_length", "eccentricity", "recovered", "acquisition_description")) cur_df <- unique(colData(cur_spe)[,c("sample_id", "recovered", "acquisition_description")]) @@ -599,7 +577,6 @@ test_that("read_steinbock function works", { expect_equal(cur_images_file$acquisition_description, cur_df$acquisition_description) - # Parallelisation #cur_spe <- read_steinbock(path, BPPARAM = BiocParallel::bpparam()) From 004a5626453a7b69731186641be1d0254f6ae380 Mon Sep 17 00:00:00 2001 From: nilseling Date: Tue, 26 Sep 2023 19:11:48 +0200 Subject: [PATCH 3/4] Adjusted unit tests for new data --- tests/testthat/test_read_cpout.R | 231 ++++++++++++---------- tests/testthat/test_show_cpout_features.R | 4 +- 2 files changed, 128 insertions(+), 107 deletions(-) diff --git a/tests/testthat/test_read_cpout.R b/tests/testthat/test_read_cpout.R index 6c00204..9976bd4 100644 --- a/tests/testthat/test_read_cpout.R +++ b/tests/testthat/test_read_cpout.R @@ -7,11 +7,12 @@ test_that("read_cpout function works.", { expect_s4_class(cur_spe, "SpatialExperiment") - expect_equal(rownames(cur_spe), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_spe), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 209)) + expect_equal(dim(cur_spe), c(5, 239)) expect_equal(names(rowData(cur_spe)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius", "ImageNumber", "Metadata_acname", "Metadata_acid", "Metadata_description")) @@ -25,9 +26,8 @@ test_that("read_cpout function works.", { object_file <- dplyr::left_join(object_file, image_file, by = "ImageNumber") expect_equal(counts(cur_spe), cur_counts * (2^16 - 1)) - expect_equal(counts(cur_spe)[1:10], c(0, 0.930232557922948, 0.0232558139480737, 0.0465116278961474, - 0.116279069740369, 0.0392156862653792, 0.813725490006618, 0.107843137229793, - 0.0588235293980688, 0.117647058796138)) + expect_equal(counts(cur_spe)[1:10], c(0.108695652148605, 0.0217391304297211, 0, 0.0434782608594421, + 0.739130434610516, 0, 0, 0, 0, 1.1999999997206)) expect_equal(cur_spe$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(cur_spe$Metadata_acname, object_file$Metadata_acname) @@ -38,6 +38,7 @@ test_that("read_cpout function works.", { cur_panel <- vroom::vroom(file.path(path, "panel.csv")) mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_spe)$Metal.Tag, cur_panel$`Metal Tag`) @@ -49,32 +50,33 @@ test_that("read_cpout function works.", { expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 3,] - expect_equal(cur_test$`First Object Number` + sum(cur_spe$sample_id %in% c("1", "2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "3")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_spe$sample_id %in% c("1", "2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "3")]) - - expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 4,] - - expect_equal(cur_test$`First Object Number` + sum(cur_spe$sample_id %in% c("1", "2", "3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "4")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_spe$sample_id %in% c("1", "2", "3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "4")]) + for (i in unique(cur_test$`First Image Number`)) { + cur_dat <- cur_spe[,cur_spe$sample_id == i] + + cur_test_dat <- cur_test[cur_test$`First Image Number` == i,] + + expect_equal(from(colPair(cur_dat, "neighborhood")), cur_test_dat$`First Object Number`) + expect_equal(to(colPair(cur_dat, "neighborhood")), cur_test_dat$`Second Object Number`) + } + + cur_dat <- unique(colData(cur_spe)[,c("sample_id", "Metadata_acname", "Metadata_acid", "Metadata_description")]) + expect_equal(as.numeric(cur_dat$sample_id), image_file$ImageNumber) + expect_equal(cur_dat$Metadata_acname, image_file$Metadata_acname) + expect_equal(cur_dat$Metadata_acid, image_file$Metadata_acid) + expect_equal(cur_dat$Metadata_description, image_file$Metadata_description) # SingleCellExperiment cur_sce <- read_cpout(path, return_as = "sce", graph_file = "Object_relationships.csv") expect_s4_class(cur_sce, "SingleCellExperiment") - expect_equal(rownames(cur_sce), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_sce), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 209)) + expect_equal(dim(cur_sce), c(5, 239)) expect_equal(names(rowData(cur_sce)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius", "ImageNumber", "Metadata_acname", @@ -88,9 +90,8 @@ test_that("read_cpout function works.", { object_file <- dplyr::left_join(object_file, image_file, by = "ImageNumber") expect_equal(counts(cur_sce), cur_counts * (2^16 - 1)) - expect_equal(counts(cur_sce)[1:10], c(0, 0.930232557922948, 0.0232558139480737, 0.0465116278961474, - 0.116279069740369, 0.0392156862653792, 0.813725490006618, 0.107843137229793, - 0.0588235293980688, 0.117647058796138)) + expect_equal(counts(cur_sce)[1:10], c(0.108695652148605, 0.0217391304297211, 0, 0.0434782608594421, + 0.739130434610516, 0, 0, 0, 0, 1.1999999997206)) expect_equal(cur_sce$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(cur_sce$Metadata_acname, object_file$Metadata_acname) @@ -101,6 +102,7 @@ test_that("read_cpout function works.", { cur_panel <- vroom::vroom(file.path(path, "panel.csv")) mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_sce)$Metal.Tag, cur_panel$`Metal Tag`) @@ -112,21 +114,15 @@ test_that("read_cpout function works.", { expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 3,] - - expect_equal(cur_test$`First Object Number` + sum(cur_sce$sample_id %in% c("1", "2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "3")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_sce$sample_id %in% c("1", "2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "3")]) - - expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 4,] - - expect_equal(cur_test$`First Object Number` + sum(cur_sce$sample_id %in% c("1", "2", "3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "4")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_sce$sample_id %in% c("1", "2", "3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "4")]) + + for (i in unique(cur_test$`First Image Number`)) { + cur_dat <- cur_sce[,cur_sce$sample_id == i] + + cur_test_dat <- cur_test[cur_test$`First Image Number` == i,] + + expect_equal(from(colPair(cur_dat, "neighborhood")), cur_test_dat$`First Object Number`) + expect_equal(to(colPair(cur_dat, "neighborhood")), cur_test_dat$`Second Object Number`) + } # Test other inputs cur_spe <- read_cpout(path, graph_file = "Object_relationships.csv", @@ -135,11 +131,12 @@ test_that("read_cpout function works.", { cur_spe <- read_cpout(path, image_file = NULL, scale_intensities = FALSE, graph_file = "Object_relationships.csv") - expect_equal(rownames(cur_spe), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_spe), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 209)) + expect_equal(dim(cur_spe), c(5, 239)) expect_equal(names(rowData(cur_spe)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius")) @@ -150,9 +147,11 @@ test_that("read_cpout function works.", { rownames(cur_counts) <- rownames(cur_spe) expect_equal(counts(cur_spe), cur_counts) - expect_equal(counts(cur_spe)[1:10], c(0, 1.41944389703662e-05, 3.54860974259155e-07, 7.09721948518309e-07, - 1.77430487129577e-06, 5.98393015417398e-07, 1.2416655069911e-05, - 1.64558079239784e-06, 8.97589523126097e-07, 1.79517904625219e-06)) + expect_equal(counts(cur_spe)[1:10], c(1.65858933621127e-06, 3.31717867242253e-07, 0, 6.63435734484507e-07, + 1.12784074862366e-05, 0, 0, 0, 0, 1.83108262717724e-05)) + + expect_equal(counts(cur_spe)[1:10] * (2^16 - 1), c(0.108695652148605, 0.0217391304297211, 0, 0.0434782608594421, + 0.739130434610516, 0, 0, 0, 0, 1.1999999997206)) expect_equal(cur_spe$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), object_file$Location_Center_X) @@ -160,6 +159,7 @@ test_that("read_cpout function works.", { cur_panel <- vroom::vroom(file.path(path, "panel.csv")) mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_spe)$Metal.Tag, cur_panel$`Metal Tag`) @@ -171,30 +171,27 @@ test_that("read_cpout function works.", { expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 3,] - - expect_equal(cur_test$`First Object Number` + sum(cur_spe$sample_id %in% c("1", "2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "3")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_spe$sample_id %in% c("1", "2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "3")]) - expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood")) - cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 4,] + for (i in unique(cur_test$`First Image Number`)) { + cur_dat <- cur_spe[,cur_spe$sample_id == i] + + cur_test_dat <- cur_test[cur_test$`First Image Number` == i,] + + expect_equal(from(colPair(cur_dat, "neighborhood")), cur_test_dat$`First Object Number`) + expect_equal(to(colPair(cur_dat, "neighborhood")), cur_test_dat$`Second Object Number`) + } - expect_equal(cur_test$`First Object Number` + sum(cur_spe$sample_id %in% c("1", "2", "3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_spe$sample_id == "4")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_spe$sample_id %in% c("1", "2", "3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_spe$sample_id == "4")]) + expect_equal(length(colPair(cur_spe, "neighborhood")), 1484) cur_sce <- read_cpout(path, return_as = "sce", image_file = NULL, scale_intensities = FALSE, graph_file = "Object_relationships.csv") - expect_equal(rownames(cur_sce), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_sce), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_sce), "counts") - expect_equal(dim(cur_sce), c(5, 209)) + expect_equal(dim(cur_sce), c(5, 239)) expect_equal(names(rowData(cur_sce)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius")) @@ -204,16 +201,16 @@ test_that("read_cpout function works.", { rownames(cur_counts) <- rownames(cur_sce) expect_equal(counts(cur_sce), cur_counts) - expect_equal(counts(cur_sce)[1:10], c(0, 1.41944389703662e-05, 3.54860974259155e-07, 7.09721948518309e-07, - 1.77430487129577e-06, 5.98393015417398e-07, 1.2416655069911e-05, - 1.64558079239784e-06, 8.97589523126097e-07, 1.79517904625219e-06)) + expect_equal(counts(cur_sce)[1:10], c(1.65858933621127e-06, 3.31717867242253e-07, 0, 6.63435734484507e-07, + 1.12784074862366e-05, 0, 0, 0, 0, 1.83108262717724e-05)) expect_equal(cur_sce$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(cur_sce$Pos_X, object_file$Location_Center_X) expect_equal(cur_sce$Pos_Y, object_file$Location_Center_Y) cur_panel <- vroom::vroom(file.path(path, "panel.csv")) - mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_sce)$Metal.Tag, cur_panel$`Metal Tag`) @@ -223,31 +220,16 @@ test_that("read_cpout function works.", { expect_equal(colPairNames(cur_sce), "neighborhood") - expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 3,] - - expect_equal(cur_test$`First Object Number` + sum(cur_sce$sample_id %in% c("1", "2")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "3")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_sce$sample_id %in% c("1", "2")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "3")]) - - expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood")) - cur_test <- vroom::vroom(file.path(path, "Object_relationships.csv")) - cur_test <- cur_test[cur_test$`First Image Number` == 4,] - - expect_equal(cur_test$`First Object Number` + sum(cur_sce$sample_id %in% c("1", "2", "3")), - from(cur_graphs)[from(cur_graphs) %in% which(cur_sce$sample_id == "4")]) - expect_equal(cur_test$`Second Object Number` + sum(cur_sce$sample_id %in% c("1", "2", "3")), - to(cur_graphs)[to(cur_graphs) %in% which(cur_sce$sample_id == "4")]) + expect_equal(length(colPair(cur_sce, "neighborhood")), 1484) cur_spe <- read_cpout(path, scale_intensities = FALSE, graph_file = "Object_relationships.csv") - expect_equal(rownames(cur_spe), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_spe), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 209)) + expect_equal(dim(cur_spe), c(5, 239)) expect_equal(names(rowData(cur_spe)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius", "ImageNumber", "Metadata_acname", "Metadata_acid", "Metadata_description")) @@ -258,9 +240,8 @@ test_that("read_cpout function works.", { rownames(cur_counts) <- rownames(cur_spe) expect_equal(counts(cur_spe), cur_counts) - expect_equal(counts(cur_spe)[1:10], c(0, 1.41944389703662e-05, 3.54860974259155e-07, 7.09721948518309e-07, - 1.77430487129577e-06, 5.98393015417398e-07, 1.2416655069911e-05, - 1.64558079239784e-06, 8.97589523126097e-07, 1.79517904625219e-06)) + expect_equal(counts(cur_spe)[1:10], c(1.65858933621127e-06, 3.31717867242253e-07, 0, 6.63435734484507e-07, + 1.12784074862366e-05, 0, 0, 0, 0, 1.83108262717724e-05)) expect_equal(cur_spe$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), object_file$Location_Center_X) @@ -268,6 +249,7 @@ test_that("read_cpout function works.", { cur_panel <- vroom::vroom(file.path(path, "panel.csv")) mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_spe)$Metal.Tag, cur_panel$`Metal Tag`) @@ -277,13 +259,16 @@ test_that("read_cpout function works.", { expect_equal(colPairNames(cur_spe), "neighborhood") + expect_equal(length(colPair(cur_spe, "neighborhood")), 1484) + cur_spe <- read_cpout(path, graph_file = NULL) - expect_equal(rownames(cur_spe), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_spe), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 209)) + expect_equal(dim(cur_spe), c(5, 239)) expect_equal(names(rowData(cur_spe)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius", "ImageNumber", "Metadata_acname", "Metadata_acid", "Metadata_description")) @@ -297,9 +282,8 @@ test_that("read_cpout function works.", { object_file <- dplyr::left_join(object_file, image_file, by = "ImageNumber") expect_equal(counts(cur_spe), cur_counts * (2^16 - 1)) - expect_equal(counts(cur_spe)[1:10], c(0, 0.930232557922948, 0.0232558139480737, 0.0465116278961474, - 0.116279069740369, 0.0392156862653792, 0.813725490006618, 0.107843137229793, - 0.0588235293980688, 0.117647058796138)) + expect_equal(counts(cur_spe)[1:10], c(0.108695652148605, 0.0217391304297211, 0, 0.0434782608594421, + 0.739130434610516, 0, 0, 0, 0, 1.1999999997206)) expect_equal(cur_spe$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(cur_spe$Metadata_acname, object_file$Metadata_acname) @@ -310,6 +294,7 @@ test_that("read_cpout function works.", { cur_panel <- vroom::vroom(file.path(path, "panel.csv")) mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_spe)$Metal.Tag, cur_panel$`Metal Tag`) @@ -321,9 +306,9 @@ test_that("read_cpout function works.", { cur_spe <- read_cpout(path, panel_file = NULL, graph_file = "Object_relationships.csv") - expect_equal(rownames(cur_spe), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_spe), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 209)) + expect_equal(dim(cur_spe), c(5, 239)) expect_equal(length(names(rowData(cur_spe))), 0) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", @@ -338,9 +323,8 @@ test_that("read_cpout function works.", { object_file <- dplyr::left_join(object_file, image_file, by = "ImageNumber") expect_equal(counts(cur_spe), cur_counts * (2^16 - 1)) - expect_equal(counts(cur_spe)[1:10], c(0, 0.930232557922948, 0.0232558139480737, 0.0465116278961474, - 0.116279069740369, 0.0392156862653792, 0.813725490006618, 0.107843137229793, - 0.0588235293980688, 0.117647058796138)) + expect_equal(counts(cur_spe)[1:10], c(0.108695652148605, 0.0217391304297211, 0, 0.0434782608594421, + 0.739130434610516, 0, 0, 0, 0, 1.1999999997206)) expect_equal(cur_spe$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(cur_spe$Metadata_acname, object_file$Metadata_acname) @@ -351,13 +335,16 @@ test_that("read_cpout function works.", { expect_equal(colPairNames(cur_spe), "neighborhood") + expect_equal(length(colPair(cur_spe, "neighborhood")), 1484) + cur_spe <- read_cpout(path, intensities = "MedianIntensity_FullStack_", graph_file = "Object_relationships.csv") - expect_equal(rownames(cur_spe), c("Sm147", "Yb172", "Pr141", "Eu153", "Ag107")) + expect_equal(rownames(cur_spe), c("Ag107", "Pr141", "Sm147", "Eu153", "Yb172")) expect_equal(assayNames(cur_spe), "counts") - expect_equal(dim(cur_spe), c(5, 209)) + expect_equal(dim(cur_spe), c(5, 239)) expect_equal(names(rowData(cur_spe)), - c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full")) + c("Tube.Number", "Metal.Tag", "Target", "ilastik", "full", "deepcell", + "cellpose")) expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "AreaShape_Area", "Neighbors_NumberOfNeighbors_8", "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius", "ImageNumber", "Metadata_acname", "Metadata_acid", "Metadata_description")) @@ -372,7 +359,7 @@ test_that("read_cpout function works.", { expect_equal(counts(cur_spe), cur_counts * (2^16 - 1)) expect_equal(counts(cur_spe)[1:10], c(0, 0, 0, 0, 0, - 0, 0, 0, 0, 0)) + 0, 0, 0, 0, 1)) expect_equal(cur_spe$Neighbors_NumberOfNeighbors_8, object_file$Neighbors_NumberOfNeighbors_8) expect_equal(cur_spe$Metadata_acname, object_file$Metadata_acname) @@ -383,6 +370,7 @@ test_that("read_cpout function works.", { cur_panel <- vroom::vroom(file.path(path, "panel.csv")) mass <- as.numeric(stringr::str_extract(cur_panel$`Metal Tag`, "[0-9]{2,3}")) + cur_panel <- cur_panel[order(as.numeric(mass), decreasing = FALSE),] expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`) expect_equal(rowData(cur_spe)$Metal.Tag, cur_panel$`Metal Tag`) @@ -392,6 +380,8 @@ test_that("read_cpout function works.", { expect_equal(colPairNames(cur_spe), "neighborhood") + expect_equal(length(colPair(cur_spe, "neighborhood")), 1484) + cur_spe <- read_cpout(path, extract_cellmetadata_from = "Location_MaxIntensity_Y_FullStack_c1", graph_file = "Object_relationships.csv") @@ -449,6 +439,37 @@ test_that("read_cpout function works.", { "AreaShape_Eccentricity", "AreaShape_MajorAxisLength", "AreaShape_MinorAxisLength", "AreaShape_MeanRadius", "ImageNumber")) + # Test other Images.csv entries + cur_spe <- read_cpout(path, graph_file = "Object_relationships.csv", + extract_imagemetadata_from = c("Intensity_PercentMaximal_FullStack_c1", + "Intensity_MeanIntensity_FullStack_c5", + "Metadata_max_x")) + + image_file <- vroom::vroom(file.path(path, "Image.csv")) + cur_test <- unique(colData(cur_spe)[,c("ImageNumber", "Intensity_PercentMaximal_FullStack_c1", + "Intensity_MeanIntensity_FullStack_c5", + "Metadata_max_x")]) + + expect_equal(image_file$ImageNumber, cur_test$ImageNumber) + expect_equal(image_file$Intensity_PercentMaximal_FullStack_c1, cur_test$Intensity_PercentMaximal_FullStack_c1) + expect_equal(image_file$Intensity_MeanIntensity_FullStack_c5, cur_test$Intensity_MeanIntensity_FullStack_c5) + expect_equal(image_file$Metadata_max_x, cur_test$Metadata_max_x) + + cur_sce <- read_cpout(path, graph_file = "Object_relationships.csv", + extract_imagemetadata_from = c("Intensity_PercentMaximal_FullStack_c1", + "Intensity_MeanIntensity_FullStack_c5", + "Metadata_max_x"), return_as = "sce") + + image_file <- vroom::vroom(file.path(path, "Image.csv")) + cur_test <- unique(colData(cur_sce)[,c("ImageNumber", "Intensity_PercentMaximal_FullStack_c1", + "Intensity_MeanIntensity_FullStack_c5", + "Metadata_max_x")]) + + expect_equal(image_file$ImageNumber, cur_test$ImageNumber) + expect_equal(image_file$Intensity_PercentMaximal_FullStack_c1, cur_test$Intensity_PercentMaximal_FullStack_c1) + expect_equal(image_file$Intensity_MeanIntensity_FullStack_c5, cur_test$Intensity_MeanIntensity_FullStack_c5) + expect_equal(image_file$Metadata_max_x, cur_test$Metadata_max_x) + # Fail expect_error(read_cpout("test", graph_file = "Object_relationships.csv"), diff --git a/tests/testthat/test_show_cpout_features.R b/tests/testthat/test_show_cpout_features.R index a9af34a..e49003b 100644 --- a/tests/testthat/test_show_cpout_features.R +++ b/tests/testthat/test_show_cpout_features.R @@ -9,7 +9,7 @@ test_that("show_cpout_features function works", { cur_df <- cur_tab$x$data expect_equal(colnames(cur_df), c(" ", "column_name", "category", "image_name", "object_name", "feature_name", "channel", "parameters", "channel_id", "data_type")) - expect_equal(unique(cur_df$channel_id), c(NA, "Sm147", "Yb172", "Pr141", "Eu153", "Ag107", "CellCenter", + expect_equal(unique(cur_df$channel_id), c(NA, "Ag107", "Pr141", "Sm147", "Eu153", "Yb172", "CellCenter", "CellBorder", "Background")) expect_equal(head(cur_df$column_name), c("Location_Center_X", "Location_Center_Y", "Location_Center_Z", "Number_Object_Number", "Neighbors_NumberOfNeighbors_8", @@ -22,7 +22,7 @@ test_that("show_cpout_features function works", { cur_df <- cur_tab$x$data expect_equal(colnames(cur_df), c(" ", "column_name", "category", "image_name", "object_name", "feature_name", "channel", "parameters", "channel_id", "data_type")) - expect_equal(unique(cur_df$channel_id), c(NA, "Sm147", "Yb172", "Pr141", "Eu153", "Ag107", "CellCenter", + expect_equal(unique(cur_df$channel_id), c(NA, "Ag107", "Pr141", "Sm147", "Eu153", "Yb172", "CellCenter", "CellBorder", "Background")) expect_equal(head(cur_df$column_name), c("Group_Number", "Group_Index", "ModuleError_01Images", "ExecutionTime_01Images", "Metadata_", "Metadata_template")) From dcc5bda84d3bac003e445006e6aca32910c62bb1 Mon Sep 17 00:00:00 2001 From: nilseling Date: Tue, 26 Sep 2023 20:26:09 +0200 Subject: [PATCH 4/4] Small update to test --- tests/testthat/test_integration_interactions.R | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/tests/testthat/test_integration_interactions.R b/tests/testthat/test_integration_interactions.R index ecda768..5d72e7a 100644 --- a/tests/testthat/test_integration_interactions.R +++ b/tests/testthat/test_integration_interactions.R @@ -257,7 +257,12 @@ test_that("testInteractions gives same results as neighbouRhood", { expect_equal(cur_classic$group_by, classic_aggregation$group) expect_equal(cur_classic$from_label, classic_aggregation$FirstLabel) expect_equal(cur_classic$to_label, classic_aggregation$SecondLabel) - expect_equal(cur_classic$ct[!is.na(cur_classic$ct)], classic_aggregation$ct[!is.na(cur_classic$ct)]) + + # There is one image where one cell is not connected to other cells + tmp_classic <- cur_classic[cur_classic$group_by != "1",] + tmp_aggregation <- classic_aggregation[classic_aggregation$group != "1",] + + expect_equal(tmp_classic$ct[!is.na(tmp_classic$ct)], tmp_aggregation$ct[!is.na(tmp_classic$ct)]) expect_true(all(classic_aggregation$ct[is.na(cur_classic$ct)] == 0)) patch_aggregation <- aggregate_classic_patch(labels_applied, patch_size = 3)