small-fish-gui 1.10.0__tar.gz → 1.10.2__tar.gz

{small_fish_gui-1.10.0 → small_fish_gui-1.10.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.10.0
+Version: 1.10.2
 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: Wiki, https://github.com/2Echoes/small_fish_gui/wiki
@@ -10,7 +10,7 @@ License-File: LICENSE
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Requires-Dist: aicsimageio>=4.14.0
 Requires-Dist: big-fish==0.6.2
 Requires-Dist: cellpose==3.0.7

{small_fish_gui-1.10.0 → small_fish_gui-1.10.2}/pyproject.toml

@@ -4,13 +4,13 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.10.0"
+version = "1.10.2"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]
 description = "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."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: BSD License",

{small_fish_gui-1.10.0 → small_fish_gui-1.10.2}/src/small_fish_gui/__init__.py

@@ -37,7 +37,7 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
-__version__ = "1.10.0"
+__version__ = "1.10.2"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os

{small_fish_gui-1.10.0 → small_fish_gui-1.10.2}/src/small_fish_gui/gui/_napari_widgets.py

@@ -133,7 +133,7 @@ class SegmentationReseter(NapariWidget) :
     def __init__(self, label_list: 'list[Labels]'):
         self.label_list = label_list
         if len(self.label_list) == 0 : raise ValueError("Empty label list")
-        self.save = self._get_save()
+        self.save = self._get_save(label_list)
         super().__init__()
         
     

{small_fish_gui-1.10.0 → small_fish_gui-1.10.2}/src/small_fish_gui/gui/napari_visualiser.py

@@ -55,6 +55,8 @@ def correct_spots(
     for im, color in zip(other_images, other_colors) :  
         Viewer.add_image(im, scale=scale, blending='additive', visible=False, colormap=color, contrast_limits=[im.min(), im.max()])
 
+
+
     single_layer = Viewer.add_points(  # single molecule spots; this layer can be update by user.
         spots, 
         size = 5, 
@@ -65,7 +67,7 @@ def correct_spots(
         symbol= 'disc', 
         name= 'single spots',
         features={
-            "cluster_id" : spot_cluster_id if not spot_cluster_id is None else [],
+            "cluster_id" : spot_cluster_id if not spot_cluster_id is None else [None] * len(spots),
             "end" : [True] * len(spots)
             }
         )
@@ -127,10 +129,6 @@ def correct_spots(
     Viewer.show(block=False)
     napari.run()
 
-    new_spots = np.concatenate([
-        single_layer.data,
-        single_layer.features.loc[:,["cluster_id"]].to_numpy()
-    ], axis=1).astype(int)
 
     if type(clusters) != type(None) :
         new_clusters = np.concatenate([
@@ -138,10 +136,16 @@ def correct_spots(
             cluster_layer.features.loc[:,["spot_number","cluster_id"]].to_numpy()
         ],axis=1)
 
+        new_spots = np.concatenate([
+            single_layer.data,
+            single_layer.features.loc[:,["cluster_id"]].to_numpy()
+        ], axis=1).astype(int)
+
         new_cluster_radius = widget_cluster_updater.cluster_radius
         new_min_spot_number = widget_cluster_updater.min_spot
 
-    else : 
+    else :
+        new_spots = single_layer.data 
         new_clusters = None
         new_cluster_radius = None
         new_min_spot_number = None

{small_fish_gui-1.10.0 → small_fish_gui-1.10.2}/src/small_fish_gui/pipeline/detection.py

@@ -217,16 +217,16 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
     if voxel_size is None or not user_parameters.get('voxel_size') is None:
         pass
     else :
-        detection_parameters['voxel_size'] = [int(v) for v in voxel_size]
-        detection_parameters['voxel_size_z'] = round(voxel_size[0])
-        detection_parameters['voxel_size_y'] = round(voxel_size[1])
-        detection_parameters['voxel_size_x'] = round(voxel_size[2])
+        detection_parameters['voxel_size'] = [round(v) if isinstance(v, (float,int)) else None for v in voxel_size]
+        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0]
+        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][1]
+        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][2]
 
     #Setting default spot size to 1.5 voxel
     if detection_parameters.get('spot_size') is None :
-        detection_parameters['spot_size_z'] = round(detection_parameters['voxel_size_z']*1.5) if not detection_parameters['voxel_size_z'] is None else None
-        detection_parameters['spot_size_y'] = round(detection_parameters['voxel_size_y']*1.5) if not detection_parameters['voxel_size_y'] is None else None
-        detection_parameters['spot_size_x'] = round(detection_parameters['voxel_size_x']*1.5) if not detection_parameters['voxel_size_x'] is None else None
+        detection_parameters['spot_size_z'] = round(detection_parameters['voxel_size_z']*1.5) if isinstance(detection_parameters['voxel_size_z'], (float,int)) else None
+        detection_parameters['spot_size_y'] = round(detection_parameters['voxel_size_y']*1.5) if isinstance(detection_parameters['voxel_size_y'],(float,int)) else None
+        detection_parameters['spot_size_x'] = round(detection_parameters['voxel_size_x']*1.5) if isinstance(detection_parameters['voxel_size_x'],(float,int)) else None
 
     while True :
         detection_parameters = detection_parameters_promt(
@@ -275,7 +275,8 @@ def _launch_detection(image, image_input_values: dict) :
     
     if type(threshold) == type(None) :     
         threshold = threshold_penalty * compute_auto_threshold(image, voxel_size=voxel_size, spot_radius=spot_size, log_kernel_size=log_kernel_size, minimum_distance=minimum_distance)
-    
+        threshold = max(threshold,15) # Force threshold to be at least 15 to match napari widget and to not have too many spots for weak configs
+
     filtered_image = _apply_log_filter(
         image=image,
         voxel_size=voxel_size,
@@ -827,7 +828,7 @@ def _create_threshold_slider(
             'size': 5, 
             'scale' : scale, 
             'face_color' : 'transparent', 
-            'edge_color' : 'red', 
+            'border_color' : 'red', 
             'symbol' : 'disc', 
             'opacity' : 0.7, 
             'blending' : 'translucent',