small-fish-gui 1.0.0__py3-none-any.whl

small_fish_gui/pipeline/main.py

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+#### New version for main.py
+import pandas as pd
+import PySimpleGUI as sg
+from ..gui import hub_prompt
+from .actions import add_detection, save_results, compute_colocalisation
+
+#'Global' parameters
+user_parameters = dict() # Very important object containg all choice from user that will influence the behavior of the main loop.
+acquisition_id = -1
+result_df = pd.DataFrame()
+cell_result_df = pd.DataFrame()
+coloc_df = pd.DataFrame()
+segmentation_done = False
+cytoplasm_label = None
+nucleus_label = None
+
+while True : #Break this loop to close small_fish
+    try :
+        event, values = hub_prompt(result_df, segmentation_done)
+
+        if event == 'Add detection' :
+
+            new_result_df, new_cell_result_df, acquisition_id, user_parameters, segmentation_done, cytoplasm_label, nucleus_label =  add_detection(
+                user_parameters=user_parameters,
+                segmentation_done=segmentation_done,
+                acquisition_id=acquisition_id,
+                cytoplasm_label = cytoplasm_label,
+                nucleus_label = nucleus_label,
+                )
+            result_df = pd.concat([result_df, new_result_df], axis=0)
+            cell_result_df = pd.concat([cell_result_df, new_cell_result_df], axis=0)
+
+        elif event == 'Save results' :
+            save_results(
+                result_df=result_df,
+                cell_result_df=cell_result_df,
+                coloc_df=coloc_df
+            )
+            
+        elif event == 'Compute colocalisation' :
+            result_tables = values.setdefault('result_table', []) #Contains the lines selected by the user on the sum-up array.
+
+            res_coloc= compute_colocalisation(
+                result_tables,
+                result_dataframe=result_df
+            )
+
+            coloc_df = pd.concat(
+                [coloc_df,res_coloc],
+                axis= 0)
+
+        elif event == "Reset results" :
+            result_df = pd.DataFrame()
+            cell_result_df = pd.DataFrame()
+            coloc_df = pd.DataFrame()
+            acquisition_id = -1
+            segmentation_done = False
+            cytoplasm_label = None
+            nucleus_label = None
+
+        elif event == "Reset segmentation" :
+            segmentation_done = False
+            cytoplasm_label = None
+            nucleus_label = None
+
+        elif event == "Delete acquisitions" :
+        #TODO
+            pass
+
+        elif event == "Batch detection" :
+        #TODO
+            pass
+        
+        else :
+            break
+
+    except Exception as error :
+        sg.popup(str(error))
+        raise error
+quit()

small_fish_gui/pipeline/test.py

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+def yielder(n) :
+    for i in range(n) : 
+        yield i
+
+def constructor(n) :
+    def inner() :
+        return yielder(n)
+    return inner
+
+#test
+
+N = 10
+
+gen1 = yielder(N)
+
+a = constructor(10)
+
+print(type(a))
+
+gen2 = a()
+gen3 = a()
+
+print('gen1 : ', list(gen1))
+print('gen2 : ', list(gen2))
+print('gen3 : ', list(gen3))
+print('gen3 : ', list(gen3))
+
+
+#Napari test
+
+import napari
+import numpy as np
+from napari.utils.events import Event
+from napari.layers import Points
+
+seed = 0
+points_number = 500
+rand_gen = np.random.default_rng(seed=seed)
+
+im_shape = (10,1000,1000)
+scale = (1,1,1)
+
+im = np.zeros(shape=im_shape)
+
+points = np.array(
+    list(zip(
+        rand_gen.integers(0,im_shape[0],size=points_number), #Z
+        rand_gen.integers(0,im_shape[1],size=points_number), #Y
+        rand_gen.integers(0,im_shape[2],size=points_number), #X
+        )),
+    dtype= int
+)
+
+spots_number = rand_gen.integers(0,20,points_number, dtype=int)
+id_list = np.arange(points_number)
+
+Viewer = napari.Viewer(title= "test", show=False)
+Viewer.add_image(im),
+cluster_layer = Viewer.add_points(
+    points, 
+    size = 10, 
+    scale=scale, 
+    face_color= 'blue', 
+    opacity= 0.7, 
+    symbol= 'diamond', 
+    name= 'foci', 
+    features= {"spot_number" : spots_number, "id" : id_list}, 
+    feature_defaults= {"spot_number" : 0, "id" : -1})
+
+
+class Points_callback :
+    """
+    Custom class to handle points number evolution during Napari run.
+    """
+    
+    def __init__(self, points, next_id) -> None:
+        self.points = points
+        self.next_id = next_id
+        self._set_callback()
+    
+    def __str__(self) -> str:
+        string = 'Points_callback object state :\ncurrent_points_number : {0}\ncurrnet_id : {1}'.format(self.current_points_number, self.next_id)
+        return string
+    
+    def get_points(self) :
+        return self.points
+    
+    def get_next_id(self) : 
+        return self.next_id
+    
+    def _set_callback(self) :
+        def callback(event:Event) :
+
+            old_points = self.get_points()
+            new_points:Points = event.source.data
+            features = event.source.features
+            
+            current_point_number = len(old_points)
+            next_id = self.get_next_id()
+            new_points_number = len(new_points)
+
+            if new_points_number > current_point_number :
+                features.at[new_points_number - 1, "id"] = next_id
+                self.next_id += 1
+
+            #preparing next callback
+            self.points = new_points
+            self._set_callback()
+        self.callback = callback
+
+live_points_number = len(points)
+next_point_id = id_list[-1] + 1
+_callback = Points_callback(points=points, next_id=next_point_id)
+Viewer.show(block=False)
+points_callback = Viewer.layers[1].events.data.connect((_callback, 'callback'))
+napari.run()

small_fish_gui/start.py

@@ -0,0 +1,7 @@
+import sys
+
+def main():
+    import small_fish.pipeline.main
+
+if __name__ == "__main__":
+    sys.exit(main())

small_fish_gui/utils.py

@@ -0,0 +1,55 @@
+import inspect
+
+def check_parameter(**kwargs):
+    """Check dtype of the function's parameters.
+
+    Parameters
+    ----------
+    kwargs : Type or Tuple[Type]
+        Map of each parameter with its expected dtype.
+
+    Returns
+    -------
+    _ : bool
+        Assert if the array is well formatted.
+
+    """
+    # get the frame and the parameters of the function
+    frame = inspect.currentframe().f_back
+    _, _, _, values = inspect.getargvalues(frame)
+
+    # compare each parameter with its expected dtype
+    for arg in kwargs:
+        expected_dtype = kwargs[arg]
+        parameter = values[arg]
+        if not isinstance(parameter, expected_dtype):
+            actual = "'{0}'".format(type(parameter).__name__)
+            if isinstance(expected_dtype, tuple):
+                target = ["'{0}'".format(x.__name__) for x in expected_dtype]
+                target = "(" + ", ".join(target) + ")"
+            else:
+                target = expected_dtype.__name__
+            raise TypeError("Parameter {0} should be a {1}. It is a {2} "
+                            "instead.".format(arg, target, actual))
+
+    return True
+
+
+def compute_anisotropy_coef(voxel_size) :
+    """
+    Returns tuple (anisotropy_z, anisotropy_y, 1)
+    voxel_size : tuple (z,y,x).
+    """
+
+    if not isinstance(voxel_size, (tuple, list)) : raise TypeError("Expected voxel_size tuple or list")
+    if len(voxel_size) == 2 : is_3D = False
+    elif len(voxel_size) == 3 : is_3D = True
+    else : raise ValueError("Expected 2D or 3D voxel, {0} element(s) found".format(len(voxel_size)))
+
+    if is_3D :
+        z_anisotropy = voxel_size[0] / voxel_size [2]
+        xy_anisotropy = voxel_size[1] / voxel_size [2]
+        return (z_anisotropy, xy_anisotropy, 1)
+
+    else :
+        return (voxel_size[0] / voxel_size[1], 1)

small_fish_gui-1.0.0.dist-info/METADATA

@@ -0,0 +1,57 @@
+Metadata-Version: 2.3
+Name: small_fish_gui
+Version: 1.0.0
+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
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+
+# Small Fish
+**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.
+
+Cell segmentation is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose
+
+Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
+
+Time stacks are not yet supported.
+
+## Installation
+
+It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
+
+```bash
+conda create -n small_fish python=3.8
+activate small_fish
+```
+Then download the small_fish package : 
+```bash
+pip install small_fish
+```
+<b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :
+
+```bash
+pip install napari[all]
+```
+
+## Run Small fish
+
+First activate your python environnement : 
+```bash
+activate small_fish
+```
+Then launch Small fish : 
+```bash
+python -m small_fish
+```
+## Developpement
+
+Optional features to include in future versions : 
+- batch processing
+- time stack (which would include cell tracking)
+- 3D segmentation

small_fish_gui-1.0.0.dist-info/RECORD

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small_fish_gui-1.0.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.24.2
+Root-Is-Purelib: true
+Tag: py3-none-any

small_fish_gui-1.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,24 @@
+BSD 2-Clause License
+
+Copyright (c) 2023, Floric Slimani
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND 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.