Inference bug, pandas docker version (#153)

* fix channel_name bug

* set pandas to 0.24.2 in docker requirements

* add test & update docstring for aux_utils - get_sms_im_name function

Co-authored-by: Jenny Folkesson <[email protected]>

micro_dl/utils/aux_utils.py

@@ -184,7 +184,7 @@ def get_sms_im_name(time_idx=None,
     This function is custom for the computational microscopy (SMS)
     group, who has the following file naming convention:
     File naming convention is assumed to be:
-        img_channelname_t***_p***_z***.tif
+        img_channelname_t***_p***_z***_extrafield.tif
     This function will alter list and dict in place.
 
     :param int time_idx: Time index
@@ -194,11 +194,11 @@ def get_sms_im_name(time_idx=None,
     :param str extra_field: Any extra string you want to include in the name
     :param str ext: Extension, e.g. '.png'
     :param int int2str_len: Length of string of the converted integers
-    :return st im_name: Image file name
+    :return str im_name: Image file name
     """
 
     im_name = "img"
-    if np.isnan(channel_name):
+    if not pd.isnull(channel_name):
         im_name += "_" + str(channel_name)
     if time_idx is not None:
         im_name += "_t" + str(time_idx).zfill(int2str_len)

requirements_docker.txt

@@ -4,7 +4,7 @@ natsort==6.0.0
 nose==1.3.7
 numpy==1.21.0
 opencv-python==4.4.0.40
-pandas==1.1.5
+pandas==0.24.2
 protobuf==3.20.1
 pydot==1.4.1
 PyYAML>=5.4

tests/utils/aux_utils_tests.py

@@ -95,6 +95,32 @@ def test_get_im_name():
     nose.tools.assert_equal(im_name, 'im_c2_z3_t1_p4_hej.png')
 
 
+def test_get_sms_im_name():
+    im_name = aux_utils.get_sms_im_name(
+        time_idx=0,
+        channel_name='phase',
+        slice_idx=10,
+        pos_idx=100,
+        extra_field='blub',
+        ext='.png',
+        int2str_len=3,
+    )
+    nose.tools.assert_equal(im_name, 'img_phase_t000_p100_z010_blub.png')
+
+
+def test_get_sms_im_name_nones():
+    im_name = aux_utils.get_sms_im_name(
+        time_idx=0,
+        channel_name=None,
+        slice_idx=None,
+        pos_idx=10,
+        extra_field=None,
+        ext='.jpg',
+        int2str_len=2,
+    )
+    nose.tools.assert_equal(im_name, 'img_t00_p10.jpg')
+
+
 def test_get_im_name_default():
     im_name = aux_utils.get_im_name()
     nose.tools.assert_equal(im_name, 'im.png')