small-fish-gui 1.3.0__py3-none-any.whl → 1.3.2__py3-none-any.whl

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__ = "1.3.0"
+__version__ = "1.3.2"

small_fish_gui/pipeline/_napari_wrapper.py

@@ -173,14 +173,15 @@ def show_segmentation(
     
     #Adding labels
     if type(cyto_image) != type(None) : Viewer.add_image(cyto_image, name= "cytoplasm signal", blending= 'additive', colormap='red', contrast_limits=[cyto_image.min(), cyto_image.max()])
-    if type(cyto_label) != type(None) : Viewer.add_labels(cyto_label, opacity= 0.4, blending= 'additive')
+    if type(cyto_label) != type(None) and not np.array_equal(cyto_label, nuc_label): Viewer.add_labels(cyto_label, opacity= 0.4, blending= 'additive')
     
     #Launch Napari
     Viewer.show(block=False)
     napari.run()
 
     new_nuc_label = Viewer.layers[1].data
-    if type(cyto_label) != type(None) : new_cyto_label = Viewer.layers[3].data
+    if type(cyto_label) != type(None) and not np.array_equal(cyto_label, nuc_label) : new_cyto_label = Viewer.layers[3].data
+    else : new_cyto_label = new_nuc_label
 
     return new_nuc_label, new_cyto_label
 
@@ -197,7 +198,6 @@ def threshold_selection(
     To view code for spot selection please have a look at magicgui instance created with `detection._create_threshold_slider` which is then passed to this napari wrapper as 'threshold_slider' argument.
     """
     
-    
     Viewer = napari.Viewer(title= "Small fish - Threshold selector", ndisplay=2, show=True)
     Viewer.add_image(
         data= image,

small_fish_gui/pipeline/detection.py

@@ -746,15 +746,16 @@ def _create_threshold_slider(
         logfiltered_image : np.ndarray,
         local_maxima : np.ndarray,
         default : int,
-        min : int,
-        max : int,
+        min_value : int,
+        max_value : int,
         voxel_size
 ) :
     
     if isinstance(default, float) : default = round(default)
+    min_value = max(min_value,25) #Security to avoid user put too low threshold and crashes Napari if out of memory.
 
     @magicgui(
-        threshold={'widget_type' : 'Slider', 'value' : default, 'min' : min, 'max' : max},
+        threshold={'widget_type' : 'Slider', 'value' : default, 'min' : min_value, 'max' : max_value},
         auto_call=True
     )
     def threshold_slider(threshold: int) -> LayerDataTuple:
@@ -763,8 +764,9 @@ def _create_threshold_slider(
             mask_local_max=local_maxima,
             threshold=threshold
         )[0]
+
         layer_args = {
-            'size': 7, 
+            'size': 5, 
             'scale' : voxel_size, 
             'face_color' : 'transparent', 
             'edge_color' : 'blue', 

{small_fish_gui-1.3.0.dist-info → small_fish_gui-1.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.3.0
+Version: 1.3.2
 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-1.3.0.dist-info → small_fish_gui-1.3.2.dist-info}/RECORD

@@ -1,7 +1,7 @@
 small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
 small_fish_gui/README.md,sha256=2c_homYDJXX6VsBiEs5obhBh3HpcTSMdyjLo-35WzE4,4062
 small_fish_gui/Segmentation example.jpg,sha256=opfiSbjmfF6z8kBs08sg_FNR2Om0AcMPU5sSwSLHdoQ,215038
-small_fish_gui/__init__.py,sha256=1eF6detE4uCLLHVMeTw-aRG6fjoUMdhrvnf-b48bVSk,1941
+small_fish_gui/__init__.py,sha256=vkwvswdFQp7_sDx7QOu5MxeKGSCJMZHIKohFa9CmaTI,1941
 small_fish_gui/__main__.py,sha256=EzSCoJ7jpSdK-QbzUwQLGZeQWjybNeq8VnCBucA8MZw,1372
 small_fish_gui/napari_detection_example.png,sha256=l5EZlrbXemLiGqb5inSVsD6Kko1Opz528-go-fBfrw8,977350
 small_fish_gui/requirements.txt,sha256=9OMfUAnLdHevq6w_fVoDmVmkSMJeFofkOK_86_fu9C0,321
@@ -23,16 +23,16 @@ small_fish_gui/interface/parameters.py,sha256=lUugD-4W2TZyJF3TH1q70TlktEYhhPtcPC
 small_fish_gui/interface/testing.py,sha256=MY5-GcPOUHagcrwR8A7QOjAmjZIDVC8Wz3NibLe3KQw,321
 small_fish_gui/pipeline/_colocalisation.py,sha256=peBw2Qz5m6wSejDkDz240UgvWl8ohNelrnmEgznbEsw,9635
 small_fish_gui/pipeline/_custom_errors.py,sha256=tQ-AUhgzIFpK30AZiQQrtHCHyGVRDdAoIjzL0Fk-1pA,43
-small_fish_gui/pipeline/_napari_wrapper.py,sha256=WtqxxcM4l4NsEnqU-YDvm7-KJgXlsGur1HFUWUgvuao,9124
+small_fish_gui/pipeline/_napari_wrapper.py,sha256=z5WEOlOKP-vhdawjPcfUAv3scGCilGu0UCHuSf6GCQY,9252
 small_fish_gui/pipeline/_preprocess.py,sha256=szNoav19Xo3USmiUTjcFgkMn9QK53ZOydbLV5aMFLws,10676
 small_fish_gui/pipeline/_segmentation.py,sha256=M2bQzgzw7Zt_DBeM3qvI0V4Pn0HFLwj0l8yV8M5aToo,12977
 small_fish_gui/pipeline/_signaltonoise.py,sha256=7A9t7xu7zghI6cr201Ldm-LjJ5NOuP56VSeJ8KIzcUo,8497
 small_fish_gui/pipeline/actions.py,sha256=EIGIOlwJ_DADX1NcLWwrTP_AidDX-4f4ggZV0gkIb58,7988
-small_fish_gui/pipeline/detection.py,sha256=sZjcDeHujdmXHVifI_Ir0xudb30Y1cuJxI6YGtp4mRQ,31778
+small_fish_gui/pipeline/detection.py,sha256=OmdIm31rtkBADwnGOTjB2EHWMLAfKer7bOXbhYPqUV8,31920
 small_fish_gui/pipeline/main.py,sha256=AAW-zK3b7Ece9cdHn9y6QG8lTa1HXG-8JtnvJ3m0HwA,3149
 small_fish_gui/pipeline/spots.py,sha256=yHvqf1eD25UltELpzcouYXhLkxiXI_mOL1ANSzXK5pw,1907
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
-small_fish_gui-1.3.0.dist-info/METADATA,sha256=i9buygANVdkEX6uNgJjUIiQU_0xxPTg3tsWFMfxZxw0,2567
-small_fish_gui-1.3.0.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-small_fish_gui-1.3.0.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-1.3.0.dist-info/RECORD,,
+small_fish_gui-1.3.2.dist-info/METADATA,sha256=BDjB5-pGaoIFhh9ujjgQCAZgKn24l6rfMEYQRuocHQk,2567
+small_fish_gui-1.3.2.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+small_fish_gui-1.3.2.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-1.3.2.dist-info/RECORD,,