small-fish-gui 2.1.4__py3-none-any.whl → 2.1.5__py3-none-any.whl

small_fish_gui/__init__.py

@@ -37,8 +37,8 @@ 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__ = "2.1.4"
-__wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
+__version__ = "2.1.5"
+__wiki__ = "https://github.com/SmallFishGUI/small_fish_gui/wiki"
 
 import os, platform
 system_type = platform.system()

small_fish_gui/batch/values.txt

@@ -0,0 +1,65 @@
+List of keys for batch 'values' dict instance :
+
+Batch_folder 
+0
+image_path 
+3D stack 
+multichannel 
+Dense regions deconvolution 
+do_cluster_computation 
+Segmentation 
+Napari correction 
+x 
+y 
+z 
+c 
+t 
+cyto_model_name 
+cytoplasm_channel 
+cytoplasm_diameter 
+nucleus_model_name 
+nucleus channel 
+nucleus_diameter 
+segment_only_nuclei 
+show_segmentation 
+saving path 
+filename 
+threshold 
+threshold penalty 
+channel to compute 
+voxel_size_z 
+voxel_size_y 
+voxel_size_x 
+spot_size_z 
+spot_size_y 
+spot_size_x 
+log_kernel_size_z 
+log_kernel_size_y 
+log_kernel_size_x 
+minimum_distance_z 
+minimum_distance_y 
+minimum_distance_x 
+nucleus channel signal 
+alpha 
+beta 
+gamma 
+deconvolution_kernel_z 
+deconvolution_kernel_y 
+deconvolution_kernel_x 
+cluster size 
+min number of spots 
+show_interactive_threshold_selector 
+spots_extraction_folder 
+spots_filename 
+do_spots_csv 
+do_spots_excel 
+do_spots_feather 
+output_folder 
+batch_name 
+save segmentation 
+save detection 
+extract spots 
+csv 
+xlsx 
+feather 
+2

small_fish_gui/gui/napari_visualiser.py

@@ -19,6 +19,7 @@ from ..utils import compute_anisotropy_coef
 def correct_spots(
         image, 
         spots, 
+        segment_only_nuclei,
         voxel_size= (1,1,1), 
         clusters= None, 
         spot_cluster_id= None, 
@@ -26,7 +27,7 @@ def correct_spots(
         min_spot_number=0, 
         cell_label= None, 
         nucleus_label= None, 
-        other_images =[]
+        other_images =[],
         ):
     """
     Open Napari viewer for user to visualize and corrects spots, clusters.
@@ -98,12 +99,32 @@ def correct_spots(
             feature_defaults= {"spot_number" : min_spot_number, "cluster_id" : -2, "end" : True} # napari features default will not work with np.nan passing -2 instead.
         )
 
-    if type(cell_label) != type(None) and not np.array_equal(nucleus_label, cell_label) : 
-        cell_label_layer = Viewer.add_labels(cell_label, scale=scale, opacity= 0.2, blending= 'additive')
-    if type(nucleus_label) != type(None) : 
+    if type(nucleus_label) != type(None) :
         nucleus_label_layer = Viewer.add_labels(nucleus_label, scale=scale, opacity= 0.2, blending= 'additive')
+        nucleus_label_layer.preserve_labels = True
+        labels_layer_list = [nucleus_label_layer]
     
+    if type(cell_label) != type(None) and not segment_only_nuclei : 
+        cell_label_layer = Viewer.add_labels(cell_label, scale=scale, opacity= 0.2, blending= 'additive')
+        cell_label_layer.preserve_labels = True
+        labels_layer_list += [cell_label_layer]
+
     #Adding widget
+    if type(nucleus_label) != type(None) : 
+        label_reseter = SegmentationReseter(labels_layer_list)
+        label_eraser = CellLabelEraser(labels_layer_list)
+        label_picker = FreeLabelPicker(labels_layer_list)
+        label_reseter = SegmentationReseter(labels_layer_list)
+        changes_applier = ChangesPropagater(labels_layer_list)
+
+        buttons_container = widgets.Container(widgets=[label_picker.widget, label_reseter.widget], labels=False, layout='horizontal')
+        changes_applier = widgets.Container(widgets=[changes_applier.widget], labels=False, layout='horizontal')
+        seg_tools_container = widgets.Container(
+            widgets = [buttons_container, changes_applier, label_eraser.widget],
+            labels=False,
+        )
+        Viewer.window.add_dock_widget(seg_tools_container, name='Segmentation', area='left')
+
     if type(clusters) != type(None) :
         initialize_all_cluster_wizards(
             single_layer=single_layer,
@@ -131,7 +152,8 @@ def correct_spots(
             widgets = [updater_container, buttons_container],
             labels=False,
         )
-        Viewer.window.add_dock_widget(tools_container, name='SmallFish', area='left')
+
+        Viewer.window.add_dock_widget(tools_container, name='Cluster', area='left', tabify=True)
 
     Viewer.show(block=False)
     napari.run()
@@ -158,8 +180,10 @@ def correct_spots(
         new_min_spot_number = None
 
     #Preparing updated segmentation masks
-    if type(cell_label) != type(None) and not np.array_equal(nucleus_label, cell_label) : 
+    if type(cell_label) != type(None) and not segment_only_nuclei : 
         new_cell_label = cell_label_layer.data
+    elif type(nucleus_label) != type(None) and segment_only_nuclei :
+        new_cell_label = nucleus_label_layer.data
     else :
         new_cell_label = cell_label
     if type(nucleus_label) != type(None) :

small_fish_gui/interface/settings.json

@@ -1,5 +1,5 @@
 {
-    "working_directory": "/media/SSD_floricslimani",
+    "working_directory": "/home/floric/Documents/fish_images",
     "do_background_removal": false,
     "background_channel": 0,
     "multichannel_stack": true,
@@ -32,7 +32,7 @@
     "do_dense_regions_deconvolution": false,
     "do_cluster": false,
     "show_napari_corrector": true,
-    "interactive_threshold_selector": false,
+    "interactive_threshold_selector": true,
     "alpha": 0.5,
     "beta": 1.0,
     "gamma": 3.0,
@@ -41,7 +41,7 @@
     "coloc_range": 400,
     "do_csv": false,
     "do_excel": false,
-    "spot_extraction_folder": "/home/floric",
+    "spot_extraction_folder": "/home/floric/my_projects/small_fish_gui",
     "voxel_size": [
         1,
         2,

small_fish_gui/pipeline/detection.py

@@ -662,18 +662,19 @@ def launch_detection(
         spots_cluster_id = None
 
     if user_parameters['show_napari_corrector'] :
-
+        
         spots, clusters, new_cluster_radius, new_min_spot_number, nucleus_label, cell_label = correct_spots(
             image, 
             spots, 
-            user_parameters['voxel_size'],
+            voxel_size=user_parameters['voxel_size'],
             clusters=clusters,
             spot_cluster_id = spots_cluster_id,
             cluster_size= user_parameters.get('cluster_size'),
             min_spot_number= user_parameters.setdefault('min_number_of_spots', 0),
             cell_label=cell_label,
             nucleus_label=nucleus_label,
-            other_images=other_image
+            other_images=other_image,
+            segment_only_nuclei=user_parameters['segment_only_nuclei'],
             )
         
         if type(new_cluster_radius) != type(None) :