small-fish-gui 1.7.1__py3-none-any.whl → 1.8.1__py3-none-any.whl

small_fish_gui/pipeline/{_segmentation.py → segmentation.py}

@@ -4,11 +4,14 @@ Contains cellpose wrappers to segmentate images.
 
 from cellpose.core import use_gpu
 from skimage.measure import label
+from ..hints import pipeline_parameters
 from ..gui.layout import _segmentation_layout
 from ..gui import prompt, prompt_with_help, ask_cancel_segmentation
 from ..interface import open_image
 from ..gui.napari import show_segmentation as napari_show_segmentation
 from .utils import from_label_get_centeroidscoords
+from ._preprocess import ask_input_parameters
+from ._preprocess import map_channels, reorder_shape, reorder_image_stack
 from matplotlib.colors import ListedColormap
 
 import matplotlib as mpl
@@ -21,7 +24,7 @@ import PySimpleGUI as sg
 import matplotlib.pyplot as plt
 import os
 
-def launch_segmentation(image: np.ndarray, user_parameters: dict) :
+def launch_segmentation(user_parameters: pipeline_parameters, nucleus_label, cytoplasm_label) :
     """
     Ask user for necessary parameters and perform cell segmentation (cytoplasm + nucleus) with cellpose.
 
@@ -32,24 +35,39 @@ def launch_segmentation(image: np.ndarray, user_parameters: dict) :
 
     Returns
     -------
-        cytoplasm_label, nucleus_label
+        cytoplasm_label, nucleus_label, user_parameters
     """
 
+    segmentation_parameters = user_parameters.copy()
+
+    #Ask for image parameters
+    new_parameters = ask_input_parameters(ask_for_segmentation= True) #The image is open and stored inside user_parameters
+    if type(new_parameters) == type(None) : #if user clicks 'Cancel'
+        return nucleus_label , cytoplasm_label, user_parameters
+    else :
+        segmentation_parameters.update(new_parameters)
+
+    map_ = map_channels(segmentation_parameters)
+    if type(map_) == type(None) : #User clicks Cancel 
+        return nucleus_label, cytoplasm_label, user_parameters
+    segmentation_parameters['reordered_shape'] = reorder_shape(segmentation_parameters['shape'], map_)
+    image = reorder_image_stack(map_, segmentation_parameters['image'])
+
     while True : # Loop if show_segmentation 
         #Default parameters
-        cyto_model_name = user_parameters.setdefault('cyto_model_name', 'cyto3')
-        cyto_size = user_parameters.setdefault('cytoplasm diameter', 180)
-        cytoplasm_channel = user_parameters.setdefault('cytoplasm channel', 0)
-        nucleus_model_name = user_parameters.setdefault('nucleus_model_name', 'nuclei')
-        nucleus_size = user_parameters.setdefault('nucleus diameter', 130)
-        nucleus_channel = user_parameters.setdefault('nucleus channel', 0)
-        other_nucleus_image = user_parameters.setdefault('other_nucleus_image',None)
+        cyto_model_name = segmentation_parameters.setdefault('cyto_model_name', 'cyto3')
+        cyto_size = segmentation_parameters.setdefault('cytoplasm diameter', 180)
+        cytoplasm_channel = segmentation_parameters.setdefault('cytoplasm channel', 0)
+        nucleus_model_name = segmentation_parameters.setdefault('nucleus_model_name', 'nuclei')
+        nucleus_size = segmentation_parameters.setdefault('nucleus diameter', 130)
+        nucleus_channel = segmentation_parameters.setdefault('nucleus channel', 0)
+        other_nucleus_image = segmentation_parameters.setdefault('other_nucleus_image',None)
         path = os.getcwd()
-        show_segmentation = user_parameters.setdefault('show segmentation', False)
-        segment_only_nuclei = user_parameters.setdefault('Segment only nuclei', False)
-        filename = user_parameters['filename']
+        show_segmentation = segmentation_parameters.setdefault('show segmentation', False)
+        segment_only_nuclei = segmentation_parameters.setdefault('Segment only nuclei', False)
+        filename = segmentation_parameters['filename']
         available_channels = list(range(image.shape[0]))
-        multichannel = user_parameters.get('multichannel')
+        multichannel = segmentation_parameters.get('is_multichannel')
 
 
     #Ask user for parameters
@@ -260,7 +278,7 @@ def launch_segmentation(image: np.ndarray, user_parameters: dict) :
 
         
     user_parameters.update(values)
-    return cytoplasm_label, nucleus_label, user_parameters
+    return nucleus_label, cytoplasm_label, user_parameters
 
 def cell_segmentation(
         image, cyto_model_name, 

small_fish_gui/pipeline/spots.py

@@ -5,7 +5,7 @@ Sub-module to handle individual spot extraction.
 
 import numpy as np
 import pandas as pd
-from ..interface.output import write_results
+from ..interface.inoutput import write_results
 
 def launch_spots_extraction(
         acquisition_id,
@@ -42,6 +42,9 @@ def compute_Spots(
         cell_label = None,
 ) :
 
+    if len(spots) == 0 :
+        return pd.DataFrame()
+
     index = list(zip(*spots))
     index = tuple(index)
     spot_intensities_list = list(image[index])

{small_fish_gui-1.7.1.dist-info → small_fish_gui-1.8.1.dist-info}/METADATA

@@ -1,11 +1,10 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.7.1
+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
 Author-email: Slimani Floric <floric.slimani@live.com>
-License-File: LICENSE
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3

small_fish_gui-1.8.1.dist-info/RECORD

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+small_fish_gui/README.md,sha256=4RpEXKZW5vH6sUWeZb88yr1TLLPi20PqOk7KdA9O9Hk,4234
+small_fish_gui/Segmentation example.jpg,sha256=opfiSbjmfF6z8kBs08sg_FNR2Om0AcMPU5sSwSLHdoQ,215038
+small_fish_gui/__init__.py,sha256=biAaT2rtp7S5QW4_IUAfG4ey2uKsf3c8m7gqNFezrj4,1941
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{small_fish_gui-1.7.1.dist-info → small_fish_gui-1.8.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.25.0
+Generator: hatchling 1.26.3
 Root-Is-Purelib: true
 Tag: py3-none-any

small_fish_gui/batch/values.py

@@ -1,3 +0,0 @@
-a = {'Batch_folder': '', 0: [], 'image path': '', '3D stack': False, 'multichannel': False, 'Dense regions deconvolution': False, 'Cluster computation': False, 'Segmentation': False, 'Napari correction': False, 'x': '0', 'y': '0', 'z': '0', 'c': '0', 't': '0', 'cyto_model_name': 'cyto3', 'cytoplasm channel': '0', 'cytoplasm diameter': '30', 'nucleus_model_name': 'nuclei', 'nucleus channel': '0', 'nucleus diameter': '30', 'Segment only nuclei': False, 'show segmentation': False, 'saving path': '', 'filename': 'cell_segmentation.png', 'threshold': '', 'threshold penalty': '1', 'channel to compute': '', 'voxel_size_z': 'z', 'voxel_size_y': 'y', 'voxel_size_x': 'x', 'spot_size_z': 'z', 'spot_size_y': 'y', 'spot_size_x': 'x', 'log_kernel_size_z': 'z', 'log_kernel_size_y': 'y', 'log_kernel_size_x': 'x', 'minimum_distance_z': 'z', 'minimum_distance_y': 'y', 'minimum_distance_x': 'x', 'nucleus channel signal': '(0,)', 'alpha': '0.5', 'beta': '1', 'gamma': '5', 'deconvolution_kernel_z': 'z', 'deconvolution_kernel_y': 'y', 'deconvolution_kernel_x': 'x', 'cluster size': '400', 'min number of spots': '5', 'Interactive threshold selector': False, 'spots_extraction_folder': '', 'spots_filename': 'spots_extraction', 'do_spots_csv': False, 'do_spots_excel': False, 'do_spots_feather': False, 'output_folder': '', 'batch_name': '', 'save segmentation': False, 'save detection': False, 'extract spots': False, 'csv': False, 'xlsx': False, 'feather': True, 2: 'Output'}
-for k in a.keys() :
-    print(k, ' : ', type(k))

small_fish_gui/docs/conf.py

@@ -1 +0,0 @@
-#init conf file

small_fish_gui/interface/parameters.py

@@ -1,2 +0,0 @@
-def ask_user_parameters() :
-    pass

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