small-fish-gui 1.3.0__tar.gz → 1.3.1__tar.gz

{small_fish_gui-1.3.0 → small_fish_gui-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.3.0
+Version: 1.3.1
 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-1.3.0 → small_fish_gui-1.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.3.0"
+version = "1.3.1"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

{small_fish_gui-1.3.0 → small_fish_gui-1.3.1}/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__ = "1.3.0"
+__version__ = "1.3.1"

{small_fish_gui-1.3.0 → small_fish_gui-1.3.1}/src/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
 
@@ -197,6 +198,7 @@ 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.
     """
     
+    print(voxel_size)
     
     Viewer = napari.Viewer(title= "Small fish - Threshold selector", ndisplay=2, show=True)
     Viewer.add_image(

{small_fish_gui-1.3.0 → small_fish_gui-1.3.1}/src/small_fish_gui/pipeline/detection.py

@@ -763,8 +763,10 @@ def _create_threshold_slider(
             mask_local_max=local_maxima,
             threshold=threshold
         )[0]
+
+        print(voxel_size)
         layer_args = {
-            'size': 7, 
+            'size': 5, 
             'scale' : voxel_size, 
             'face_color' : 'transparent', 
             'edge_color' : 'blue',