small-fish-gui 1.8.0__tar.gz → 1.8.1__tar.gz

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.8.0
+Version: 1.8.1
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 Project-URL: Homepage, https://github.com/2Echoes/small_fish
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.8.0"
+version = "1.8.1"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/src/small_fish_gui/__init__.py

@@ -38,4 +38,4 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 """
-__version__ = "1.8.0"
+__version__ = "1.8.1"

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/src/small_fish_gui/batch/pipeline.py

@@ -137,7 +137,10 @@ def batch_pipeline(
                 raise(error)
         
         if parameters['save detection'] :
-            if parameters['do_cluster_computation'] : spots_list = [spots, clusters[:,:parameters['dim']]]
+            if parameters['do_cluster_computation'] : 
+                if len(clusters) > 0 :
+                    spots_list = [spots, clusters[:,:parameters['dim']]]
+                else : spots_list = [spots]
             else : spots_list = [spots]
             output_spot_tiffvisual(
                 image,

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/src/small_fish_gui/batch/prompt.py

@@ -45,18 +45,18 @@ def batch_promp(
     #Input tab
     input_layout = _input_parameters_layout(
         ask_for_segmentation=True,
-        is_3D_stack_preset= preset.setdefault("3D stack" ,False),
+        is_3D_stack_preset= preset.setdefault("is_3D_stack" ,False),
         time_stack_preset=False,
-        multichannel_preset=preset.setdefault("multichannel" ,False),
-        do_dense_regions_deconvolution_preset=preset.setdefault("Dense regions deconvolution" ,False),
+        multichannel_preset=preset.setdefault("is_multichannel" ,False),
+        do_dense_regions_deconvolution_preset=preset.setdefault("do_dense_regions_deconvolution" ,False),
         do_clustering_preset= preset.setdefault("do_cluster_computation", False),
         do_Napari_correction=False,
-        do_segmentation_preset= preset.setdefault("Segmentation", False),
+        do_segmentation_preset= preset.setdefault("segmentation_done", False),
     )
     input_layout += [[sg.Button('Ok')]]
     input_tab = sg.Tab("Input", input_layout)
 
-    napari_correction_elmt = get_elmt_from_key(input_tab, key='Napari correction')
+    napari_correction_elmt = get_elmt_from_key(input_tab, key='show_napari_corrector')
 
     #Maptab
     map_layout = _ask_channel_map_layout(
@@ -86,7 +86,7 @@ def batch_promp(
     
     apply_segmentation_button = sg.Button('apply', key='apply-segmentation')
     segmentation_layout += [[apply_segmentation_button]]
-    seg_keys_to_hide = ['show segmentation', 'saving path', 'filename']
+    seg_keys_to_hide = ['show segmentation', 'saving path', 'filename', 'other_nucleus_image']
     segmentation_tab = sg.Tab("Segmentation", segmentation_layout, visible=False)
 
     #Detection tab
@@ -228,10 +228,10 @@ def batch_promp(
                 print("Welcome to small fish batch analysis. Please start by loading some files and setting parameters.")
 
             batch_folder = values.get('Batch_folder')
-            is_multichanel = values.get('multichannel')
-            is_3D = values.get('3D stack')
-            do_segmentation = values.get('Segmentation')
-            do_dense_regions_deconvolution = values.get('Dense regions deconvolution')
+            is_multichanel = values.get('is_multichannel')
+            is_3D = values.get('is_3D_stack')
+            do_segmentation = values.get('do_segmentation')
+            do_dense_regions_deconvolution = values.get('do_dense_regions_deconvolution')
             do_clustering = values.get('do_cluster_computation')
 
             if type(batch_folder) != type(None)  and event == 'Load':

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/src/small_fish_gui/gui/layout.py

@@ -227,18 +227,14 @@ def _input_parameters_layout(
 
 ) :
     layout_image_path = path_layout(['image path'], header= "Image")
-    layout_image_path += bool_layout(['is_3D_stack', 'is_multichannel'], preset= [is_3D_stack_preset, time_stack_preset, multichannel_preset])
+    layout_image_path += bool_layout(['3D stack', 'Multichannel stack'], keys=['is_3D_stack', 'is_multichannel'], preset= [is_3D_stack_preset, multichannel_preset])
     
-    if ask_for_segmentation : 
-        layout_image_path += bool_layout(
-            ['do_dense_regions_deconvolution', 'do_cluster_computation', 'Segmentation', 'show_napari_corrector'], 
-            preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_segmentation_preset, do_Napari_correction], 
-            header= "Pipeline settings")
-    else : 
-        layout_image_path += bool_layout(
-            ['do_dense_regions_deconvolution', 'do_cluster_computation', 'show_napari_corrector'], 
-            preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_Napari_correction], 
-            header= "Pipeline settings")
+    layout_image_path += bool_layout(
+        ['Dense regions deconvolution', 'Compute clusters', 'Cell segmentation', 'Open Napari corrector'],
+        keys= ['do_dense_regions_deconvolution', 'do_cluster_computation', 'do_segmentation', 'show_napari_corrector'], 
+        preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_segmentation_preset, do_Napari_correction], 
+        header= "Pipeline settings")
+
 
     return layout_image_path
 

{small_fish_gui-1.8.0 → small_fish_gui-1.8.1}/src/small_fish_gui/hints.py

@@ -8,7 +8,6 @@ class pipeline_parameters(TypedDict) :
             """
             At run time is a regular dict instance, this class is used for keys hinting
             """
-            is_3D_stack : bool
             alpha : float
             beta : float
             channel_to_compute : int
@@ -31,6 +30,7 @@ class pipeline_parameters(TypedDict) :
             minimum_distance_x : float
             minimum_distance_y : float
             minimum_distance_z : float
+            is_3D_stack : bool
             is_multichannel : bool
             show_napari_corrector : bool
             nucleus_channel_signal : int