Merge pull request #105 from SyneRBI/data-slices

SyneRBI · Sep 13, 2024 · 4a8a865 · 4a8a865
2 parents 5c1fa8a + 955bd0e
commit 4a8a865
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Showing 2 changed files with 21 additions and 23 deletions.
diff --git a/SIRF_data_preparation/dataset_settings.py b/SIRF_data_preparation/dataset_settings.py
@@ -1,7 +1,12 @@
 """Settings for recon and display used in the data preparation"""
-
 from dataclasses import dataclass
 
+from petric import DATA_SLICES
+
+DATA_SUBSETS = {
+    'Siemens_mMR_NEMA_IQ': 7, 'Siemens_mMR_ACR': 7, 'NeuroLF_Hoffman_Dataset': 16, 'Mediso_NEMA_IQ': 12,
+    'Siemens_Vision600_thorax': 5}
+
 
 @dataclass
 class DatasetSettings:
@@ -10,19 +15,4 @@ class DatasetSettings:
 
 
 def get_settings(scanID: str):
-    if scanID == 'Siemens_mMR_NEMA_IQ':
-        slices = {'transverse_slice': 72, 'coronal_slice': 109} # , 'sagittal_slice': 89}
-        num_subsets = 7
-    elif scanID == 'Siemens_mMR_ACR':
-        slices = {'transverse_slice': 99}
-        num_subsets = 7
-    elif scanID == 'NeuroLF_Hoffman_Dataset':
-        slices = {'transverse_slice': 72}
-        num_subsets = 16
-    elif scanID == 'Mediso_NEMA_IQ':
-        slices = {'transverse_slice': 22, 'coronal_slice': 89, 'sagittal_slice': 66}
-        num_subsets = 12
-    else:                                                       # Vision
-        slices = {}
-        num_subsets = 5
-    return DatasetSettings(num_subsets, slices)
+    return DatasetSettings(DATA_SUBSETS[scanID], DATA_SLICES[scanID])
diff --git a/petric.py b/petric.py
@@ -246,15 +246,23 @@ def get_image(fname):
                    whole_object_mask, background_mask, voi_masks, srcdir.resolve())
 
 
+DATA_SLICES = {
+    'Siemens_mMR_NEMA_IQ': {'transverse_slice': 72, 'coronal_slice': 109},                 # 'sagittal_slice': 89
+    'Siemens_mMR_ACR': {'transverse_slice': 99},
+    'NeuroLF_Hoffman_Dataset': {'transverse_slice': 72},
+    'Mediso_NEMA_IQ': {'transverse_slice': 22, 'coronal_slice': 89, 'sagittal_slice': 66},
+    'Siemens_Vision600_thorax': {}}
+
 if SRCDIR.is_dir():
     # create list of existing data
     # NB: `MetricsWithTimeout` initialises `SaveIters` which creates `outdir`
-    data_dirs_metrics = [(SRCDIR / "Siemens_mMR_NEMA_IQ", OUTDIR / "mMR_NEMA",
-                          [MetricsWithTimeout(outdir=OUTDIR / "mMR_NEMA", transverse_slice=72, coronal_slice=109)]),
-                         (SRCDIR / "NeuroLF_Hoffman_Dataset", OUTDIR / "NeuroLF_Hoffman",
-                          [MetricsWithTimeout(outdir=OUTDIR / "NeuroLF_Hoffman", transverse_slice=72)]),
-                         (SRCDIR / "Siemens_Vision600_thorax", OUTDIR / "Vision600_thorax",
-                          [MetricsWithTimeout(outdir=OUTDIR / "Vision600_thorax")])]
+    data_dirs_metrics = [
+        (SRCDIR / "Siemens_mMR_NEMA_IQ", OUTDIR / "mMR_NEMA",
+         [MetricsWithTimeout(outdir=OUTDIR / "mMR_NEMA", **DATA_SLICES['Siemens_mMR_NEMA_IQ'])]),
+        (SRCDIR / "NeuroLF_Hoffman_Dataset", OUTDIR / "NeuroLF_Hoffman",
+         [MetricsWithTimeout(outdir=OUTDIR / "NeuroLF_Hoffman", **DATA_SLICES['NeuroLF_Hoffman_Dataset'])]),
+        (SRCDIR / "Siemens_Vision600_thorax", OUTDIR / "Vision600_thorax",
+         [MetricsWithTimeout(outdir=OUTDIR / "Vision600_thorax", **DATA_SLICES['Siemens_Vision600_thorax'])])]
 else:
     log.warning("Source directory does not exist: %s", SRCDIR)
     data_dirs_metrics = [(None, None, [])] # type: ignore