Format update: NutriMorph can be run on a file or on multiple files within repositories

brick/component/soma.py

@@ -250,6 +250,9 @@ class soma_t(glial_cmp_t):
         '''
         #
         # Initialization
+        if somas.__len__() == 0:
+            raise AssertionError("No soma detected on the image.")
+
         shape = somas[0].img_shape
         result = np_.zeros(shape, dtype=np_.int64)
 

parameters.ini

@@ -49,20 +49,12 @@ parameter3                  :   None
 ; then your parameter has the value string: 'None', and not None
 
 [Input]
-data_path                   :   D:\\MorganeNadal\\IBA1-Microglies\\CHO_1H_D_1.70_3.3\\CHO_1H_D_1.70_3.3_1.tif
+data_path                   :   D:\\MorganeNadal\\IBA1-Microglies\\CHO_1H_D_1.70_3.3
 #D:\\MorganeNadal\\IBA1-Microglies\\CHO_1H_D_1.70_3.3\\CHO_1H_D_1.70_3.3_1.tif
 #.\data\DIO_6H_6_1.70bis_2.2_3.tif
 #D:\MorganeNadal\IBA1-Microglies\standard conditions\020620_ST8_20W_1_2.lif - Position 3.tif
 #D:\\MorganeNadal\\IBA1-Microglies\\standard conditions\\ST8_crop2(1024x1024)_vert.tif
 ; direct data path to the image
-file_path
-# D:\\MorganeNadal\\IBA1-Microglies
-; TODO path to the repository containing the different condition repository
-; Set to None if data_path exists
-conditions
-# ["CHO_1H_D_1.70_3.3", "CHO_3H_H_1.82_3.2", "CHO_6H_LL_1.70_1.3", "DIO_1H_16_1.58_2.1", "DIO_3H_F_1.82_3.1", "DIO_6H_6_1.70bis_2.2"]
-; TODO list of the repository containing the different conditions
-; Set to None if data_path exists
 channel
 ; Can take the values R, G or B.
 ; Can also be set to None (cf. README above).
@@ -71,6 +63,8 @@ size_voxel_in_micron
 #:   [0.071, 0.071, 0.4997]
 ; size_voxel_in_micron ->  [X,Y,Z]
 ; Can also be set to None (cf. README above).
+crop_image
+# TODO
 save_images
 ; # TODO if None, no saving. Otherwise, path where to save images
 

search_parameters.py

@@ -50,10 +50,9 @@ def IfNotFloat(section: str, key: str) -> Union[Union[float, str], Any]:
 
 # [Input]
 data_path = parameters['Input']['data_path']
-file_path = parameters['Input']['file_path']
-conditions = IfNotFloat('Input', 'conditions')
 channel = parameters['Input']['channel']
 size_voxel_in_micron = IfNotFloat('Input', 'size_voxel_in_micron')
+crop_image = IfNotFloat('Input', 'crop_image')
 save_images = IfNotFloat('Input', 'save_images')
 
 # [Somas]