small-fish-gui 1.9.3__py3-none-any.whl → 1.10.0__py3-none-any.whl

small_fish_gui/hints.py

@@ -1,7 +1,7 @@
 
 #Add keys hinting to user_parameters instance keys.
 
-from typing import TypedDict, Sequence
+from typing import TypedDict, Tuple
 from numpy import ndarray
     
 class pipeline_parameters(TypedDict) :
@@ -11,6 +11,7 @@ class pipeline_parameters(TypedDict) :
             alpha : float
             beta : float
             channel_to_compute : int
+            cluster_size : int
             do_cluster_computation : bool
             do_dense_regions_deconvolution : bool
             do_spots_excel : bool
@@ -22,11 +23,12 @@ class pipeline_parameters(TypedDict) :
             image_path : str
             image : ndarray
             show_interactive_threshold_selector : bool
-            log_kernel_size : 'Sequence[float,float,float]'
+            log_kernel_size : Tuple[float,float,float]
             log_kernel_size_x : float
             log_kernel_size_y : float
             log_kernel_size_z : float
-            minimum_distance : 'Sequence[float,float,float]'
+            min_number_of_spots : int
+            minimum_distance : Tuple[float,float,float]
             minimum_distance_x : float
             minimum_distance_y : float
             minimum_distance_z : float
@@ -34,13 +36,13 @@ class pipeline_parameters(TypedDict) :
             is_multichannel : bool
             show_napari_corrector : bool
             nucleus_channel_signal : int
-            reodered_shape : 'Sequence[int,int,int,int,int]'
+            reodered_shape : Tuple[int,int,int,int,int]
             do_segmentation : bool
             segmentation_done : bool
-            shape : 'Sequence[int,int,int,int,int]'
+            shape : Tuple[int,int,int,int,int]
             spots_extraction_folder : str
             spots_filename : str
-            spot_size : 'Sequence[int,int,int]'
+            spot_size : Tuple[int,int,int]
             spot_size_x : int
             spot_size_y : int
             spot_size_z : int
@@ -48,7 +50,7 @@ class pipeline_parameters(TypedDict) :
             threshold_penalty : int
             time_stack : None
             time_step : None
-            voxel_size : 'Sequence[float,float,float]'
+            voxel_size : Tuple[float,float,float]
             voxel_size_x : float
             voxel_size_y : float
             voxel_size_z : float

small_fish_gui/interface/__init__.py

@@ -6,5 +6,6 @@ from .image import open_image
 from .image import get_filename 
 from .image import check_format
 from .image import FormatError
+from .image import get_voxel_size
 
 from .inoutput import write_results

small_fish_gui/interface/image.py

@@ -2,6 +2,8 @@ from bigfish.stack import read_image
 from czifile import imread
 from ..utils import check_parameter
 import re
+from aicsimageio import AICSImage
+from typing import Optional, Tuple
 
 class FormatError(Exception):
     pass
@@ -35,4 +37,23 @@ def get_filename(full_path: str) :
     re_match = re.findall(pattern, full_path)
     if len(re_match) == 0 : raise ValueError("Could not read filename from image full path.")
     if len(re_match) == 1 : return re_match[0]
-    else : raise AssertionError("Several filenames read from path")
+    else : raise AssertionError("Several filenames read from path")
+
+def get_voxel_size(filepath: str) -> Optional[Tuple[Optional[float], Optional[float], Optional[float]]]:
+    """
+    Returns voxel size in nanometers (nm) as a tuple (X, Y, Z).
+    Any of the dimensions may be None if not available.
+    /WARINING\ : the unit might not be nm
+    """
+    try:
+        img = AICSImage(filepath)
+        voxel_sizes = img.physical_pixel_sizes  # values in meters
+        if voxel_sizes is None:
+            return None
+        x = voxel_sizes.X * 1e3 if voxel_sizes.X else None
+        y = voxel_sizes.Y * 1e3 if voxel_sizes.Y else None
+        z = voxel_sizes.Z * 1e3 if voxel_sizes.Z else None
+        return (z, y, x)
+    except Exception as e:
+        print(f"Failed to read voxel size from {filepath}: {e}")
+        return None

small_fish_gui/interface/testing.py

@@ -1,12 +1,63 @@
-import FreeSimpleGUI as sg
+import os
+from typing import Optional, Tuple
 
-layout = [
-    [sg.Radio(['A',], key='button', group_id=0, key='test1'),sg.Radio(['B'], key='button', group_id=0, key='test2'), sg.Radio(['C'], key='button', group_id=0, key='test3')],
-    [sg.Radio(['D',], key='button', group_id=1, key='test4')],
-    [sg.Button('Ok')]
-    ]
+IMAGE_PATH = "/home/floric/Documents/python/small_fish/images_test/Cropped_image_dapi_0.tif"
 
-window = sg.Window(title= 'test', layout=layout)
-event, values = window.read()
+def get_voxel_size_0(filepath: str) -> Optional[Tuple[float, float, float]]:
+    ext = os.path.splitext(filepath)[1].lower()
+    
+    if ext in ['.tif', '.tiff']:
+        import tifffile
+        with tifffile.TiffFile(filepath) as tif:
+            tags = tif.pages[0].tags
+            print(tags)
+            x_res = tags.get('XResolution')
+            y_res = tags.get('YResolution')
+            if x_res and y_res:
+                # Resolution is typically in (numerator, denominator)
+                x = x_res.value[1] / x_res.value[0]
+                y = y_res.value[1] / y_res.value[0]
+                # Microscopy images may store pixel size in microns per pixel (invert if necessary)
+                return (1.0, y, x)  # Z usually not in TIFF metadata, so set as 1.0 or None
+            return None
+    
+    elif ext == '.czi':
+        import czifile
+        with czifile.CziFile(filepath) as czi:
+            metadata = czi.metadata(raw=False)
+            scaling = metadata.get('ImageDocument', {}).get('Metadata', {}).get('Scaling', {})
+            try:
+                x = float(scaling['Items']['Distance'][0]['Value']) * 1e6  # in microns
+                y = float(scaling['Items']['Distance'][1]['Value']) * 1e6
+                z = float(scaling['Items']['Distance'][2]['Value']) * 1e6 if len(scaling['Items']['Distance']) > 2 else 1.0
+                return (x, y, z)
+            except Exception:
+                return None
+    
+    return None
 
-print(values)
+from aicsimageio import AICSImage
+from typing import Optional, Tuple
+
+def get_voxel_size(filepath: str) -> Optional[Tuple[Optional[float], Optional[float], Optional[float]]]:
+    """
+    Returns voxel size in nanometers (nm) as a tuple (X, Y, Z).
+    Any of the dimensions may be None if not available.
+    /WARINING\ : the unit might not be nm
+    """
+    try:
+        img = AICSImage(filepath)
+        voxel_sizes = img.physical_pixel_sizes  # values in meters
+        if voxel_sizes is None:
+            return None
+        x = voxel_sizes.X * 1e3 if voxel_sizes.X else None
+        y = voxel_sizes.Y * 1e3 if voxel_sizes.Y else None
+        z = voxel_sizes.Z * 1e3 if voxel_sizes.Z else None
+        return (x, y, z)
+    except Exception as e:
+        print(f"Failed to read voxel size from {filepath}: {e}")
+        return None
+
+
+res = get_voxel_size("/home/floric/Documents/python/small_fish/images_test/Cropped_image_dapi_0.tif")
+print("RES : ",res)

small_fish_gui/pipeline/_preprocess.py

@@ -1,8 +1,8 @@
 import numpy as np
 import os
 import FreeSimpleGUI as sg
-from ..gui import _error_popup, _warning_popup, parameters_layout, add_header, prompt, prompt_with_help
-from ..gui.prompts import input_image_prompt
+from ..gui import _error_popup, _warning_popup, parameters_layout, add_header
+from ..gui.prompts import input_image_prompt, prompt
 
 class ParameterInputError(Exception) :
     """
@@ -141,7 +141,7 @@ def _ask_channel_map(shape, is_3D_stack, is_time_stack, multichannel, preset_map
         if multichannel : layout += [parameters_layout(['c'], default_values=[c])]
         if is_time_stack : layout += [parameters_layout(['t'], default_values=[t])]
 
-        event, preset_map = prompt_with_help(layout,help= 'mapping', add_scrollbar=False)
+        event, preset_map = prompt(layout, add_scrollbar=False)
         if event == 'Cancel' : return save_preset
 
         #Check integrity
@@ -169,7 +169,7 @@ def _show_mapping(shape, map_, is_3D_stack, is_time_stack, multichannel) :
             [sg.Button('Change mapping')]
         ]
 
-        event, values = prompt_with_help(layout, help='mapping', add_scrollbar=False)
+        event, values = prompt(layout, add_scrollbar=False)
 
         if event == 'Ok' :
             return map_
@@ -186,20 +186,26 @@ def convert_parameters_types(values:dict) :
     """
 
     #Tuples
-    tuples_list = ['voxel_size', 'spot_size', 'log_kernel_size', 'minimum_distance', 'deconvolution_kernel']
+    tuples_dict = {
+        'voxel_size' : int,
+        'spot_size' : float, 
+        'log_kernel_size' : float, 
+        'minimum_distance' : float, 
+        'deconvolution_kernel' : float,
+        }
     dim = values['dim']
     if dim == 3 : dim_tuple = ('z', 'y', 'x')
     else : dim_tuple = ('y', 'x')
 
-    for tuple_parameter in tuples_list :
+    for tuple_parameter, type_cast in tuples_dict.items() :
         try :
-            tuple_values = tuple([float(values.get(tuple_parameter + '_{0}'.format(dimension))) for dimension in dim_tuple])
+            tuple_values = tuple([type_cast(values.get(tuple_parameter + '_{0}'.format(dimension))) for dimension in dim_tuple])
         except Exception as e : #execption when str cannot be converted to float or no parameter was given.
             values[tuple_parameter] = None
         else : values[tuple_parameter] = tuple_values
 
     #Parameters
-    int_list = ['threshold', 'channel_to_compute', 'channel_to_compute', 'min number of spots', 'cluster size','nucleus channel signal']
+    int_list = ['threshold', 'channel_to_compute', 'channel_to_compute', 'min_number_of_spots', 'cluster_size','nucleus channel signal']
     float_list = ['alpha', 'beta', 'gamma', 'threshold penalty']
 
     for parameter in int_list :
@@ -252,9 +258,9 @@ def check_integrity(
             raise ParameterInputError("alpha must be set between 0 and 1.")
 
     if do_clustering :
-        if not isinstance(values['min number of spots'], (int)) :
+        if not isinstance(values['min_number_of_spots'], (int)) :
             raise ParameterInputError("Incorrect min spot number parameter.")
-        if not isinstance(values['cluster size'], (int)) :
+        if not isinstance(values['cluster_size'], (int)) :
             raise ParameterInputError("Incorrect cluster size parameter.")
 
     #channel
@@ -339,7 +345,7 @@ def clean_unused_parameters_cache(user_parameters: dict) :
     """
     Clean unused parameters that were set to None in previous run.
     """
-    parameters = ['alpha', 'beta', 'gamma', 'cluster size', 'min number of spots']
+    parameters = ['alpha', 'beta', 'gamma', 'cluster_size', 'min_number_of_spots']
     for parameter in parameters :
         if parameter in user_parameters.keys() :
             if type(user_parameters[parameter]) == type(None) :
@@ -389,6 +395,6 @@ def ask_input_parameters(ask_for_segmentation=True) :
 
     values.update(image_input_values)
     values['dim'] = 3 if values['is_3D_stack'] else 2
-    values['filename'] = os.path.basename(values['image path'])
+    values['filename'] = os.path.basename(values['image_path'])
     
     return values

small_fish_gui/pipeline/actions.py

@@ -22,11 +22,16 @@ from .segmentation import launch_segmentation
 from ._colocalisation import initiate_colocalisation, launch_colocalisation
 
 from ..hints import pipeline_parameters
+from ..__init__ import __wiki__
 
 import os
 import pandas as pd
 import FreeSimpleGUI as sg
 import numpy as np
+import webbrowser
+
+def open_wiki() :
+    webbrowser.open_new_tab(__wiki__)
 
 def segment_cells(user_parameters : pipeline_parameters, nucleus_label, cytoplasm_label) :
     if user_parameters['segmentation_done'] :

small_fish_gui/pipeline/detection.py

@@ -3,7 +3,6 @@ Contains code to handle detection as well as bigfish wrappers related to spot de
 """
 from ..hints import pipeline_parameters
 
-
 from ._preprocess import ParameterInputError
 from ._preprocess import check_integrity, convert_parameters_types
 
@@ -11,22 +10,24 @@ from ..gui.napari_visualiser import correct_spots, threshold_selection
 from ..gui import add_default_loading
 from ..gui import detection_parameters_promt
 
+from ..interface import get_voxel_size
 from ..utils import compute_anisotropy_coef
 from ._signaltonoise import compute_snr_spots
 
 from magicgui import magicgui
+
+from types import GeneratorType
 from napari.types import LayerDataTuple
 
 import numpy as np
+from numpy import NaN
 import pandas as pd
 import FreeSimpleGUI as sg
-from numpy import NaN
 import bigfish.detection as detection
 import bigfish.stack as stack
 import bigfish.multistack as multistack
 import bigfish.classification as classification
 from bigfish.detection.spot_detection import get_object_radius_pixel
-from types import GeneratorType
 from skimage.measure import regionprops
 from scipy.ndimage import binary_dilation
 
@@ -211,6 +212,22 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
     do_clustering = user_parameters['do_cluster_computation']
     detection_parameters = user_parameters.copy()
     
+    #Attempt to read voxel size from metadata
+    voxel_size = get_voxel_size(user_parameters['image_path'])
+    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])
+
+    #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
+
     while True :
         detection_parameters = detection_parameters_promt(
             is_3D_stack=is_3D_stack,
@@ -237,6 +254,7 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
         else :
             user_parameters.update(detection_parameters)
             break
+    
     return user_parameters
 
 @add_default_loading
@@ -557,8 +575,8 @@ def launch_cell_extraction(
 def launch_clustering(spots, user_parameters : pipeline_parameters): 
 
     voxel_size = user_parameters['voxel_size']
-    nb_min_spots = user_parameters['min number of spots']
-    cluster_size = user_parameters['cluster size']
+    nb_min_spots = user_parameters['min_number_of_spots']
+    cluster_size = user_parameters['cluster_size']
 
     cluster_result_dict = cluster_detection(
         spots=spots,
@@ -622,19 +640,24 @@ def launch_detection(
 
     if user_parameters['show_napari_corrector'] :
 
-        spots, clusters = correct_spots(
+        spots, clusters, new_cluster_radius, new_min_spot_number = correct_spots(
             image, 
             spots, 
             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),
+            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
             )
         
+        if type(new_cluster_radius) != type(None) :
+            user_parameters['cluster_size'] = new_cluster_radius
+        if type(new_min_spot_number) != type(None) :
+            user_parameters['min_number_of_spots'] = new_min_spot_number
+        
         if do_clustering :
             spots, spots_cluster_id = spots[:,:-1], spots[:,-1]
         else :

small_fish_gui/pipeline/main.py

@@ -1,13 +1,22 @@
 """
 This script is called when software starts; it is the main loop.
 """
+import traceback, os
+from small_fish_gui import __version__
 
 import pandas as pd
 import FreeSimpleGUI as sg
-from ..gui import hub_prompt
-from .actions import add_detection, save_results, compute_colocalisation, delete_acquisitions, rename_acquisitions, save_segmentation, load_segmentation, segment_cells
+
+from .actions import add_detection 
+from . actions import save_results 
+from . actions import compute_colocalisation 
+from . actions import delete_acquisitions, rename_acquisitions 
+from . actions import save_segmentation, load_segmentation, segment_cells
+from .actions import open_wiki
+
 from ._preprocess import clean_unused_parameters_cache
 from ..batch import batch_promp
+from ..gui import hub_prompt, prompt_restore_main_menu
 from ..hints import pipeline_parameters
 
 #'Global' parameters
@@ -103,11 +112,39 @@ while True : #Break this loop to close small_fish
             selected_acquisitions = values.setdefault('result_table', []) #Contains the lines selected by the user on the sum-up array.
             result_df, cell_result_df, global_coloc_df, cell_coloc_df = rename_acquisitions(selected_acquisitions, result_df, cell_result_df, global_coloc_df, cell_coloc_df)
 
+        elif event == "wiki" :
+            open_wiki()
+
         else :
             break
         
 
     except Exception as error :
         sg.popup(str(error))
-        raise error
+
+        with open("error_log.txt",'a') as error_log :
+            error_log.writelines([
+                f"version {__version__}",
+                f"error : {error}",
+                f"traceback :\n{traceback.format_exc()}",
+            ])
+
+        print(f"error_log saved at {os.getcwd()}/error_log.txt. Please consider reporting this by opening an issue on github.")
+
+        save_quit = prompt_restore_main_menu()
+
+        if save_quit is None :
+            raise error
+
+        elif save_quit :
+            save_results(
+                result_df=result_df,
+                cell_result_df=cell_result_df,
+                global_coloc_df=global_coloc_df,
+                cell_coloc_df = cell_coloc_df,
+            )
+            quit()
+        else :
+            continue
+
 quit()

small_fish_gui/pipeline/segmentation.py

@@ -6,7 +6,7 @@ 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 ..gui import prompt, ask_cancel_segmentation
 from ..interface import open_image
 from ..gui.napari_visualiser import show_segmentation as napari_show_segmentation
 from .utils import from_label_get_centeroidscoords
@@ -88,7 +88,7 @@ def launch_segmentation(user_parameters: pipeline_parameters, nucleus_label, cyt
                 multichannel=multichannel,
             )
 
-            event, values = prompt_with_help(layout, help='segmentation')
+            event, values = prompt(layout)
             if event == 'Cancel' :
                 cancel_segmentation = ask_cancel_segmentation()
 

small_fish_gui/requirements.txt

@@ -2,16 +2,17 @@ big-fish==0.6.2
 cellpose==3.0.7
 czifile==2019.7.2
 imageio==2.34.0
-napari==0.4.19.post1
-napari-console==0.0.9
-napari-plugin-engine==0.2.0
-napari-plugin-manager==0.1.0a2
-napari-svg==0.1.10
-numpy==1.24.4
-pandas==1.5.3
-FreeSimpleGUI==5.1.1
-scipy==1.9.1
+napari>=0.4.19.post1
+napari-console>=0.0.9
+napari-plugin-engine>=0.2.0
+napari-plugin-manager>=0.1.0a2
+napari-svg>=0.1.10
+numpy>=1.24.4
+pandas>=1.5.3
+FreeSimpleGUI>=5.1.1
+scipy>=1.9.1
 scikit-image==0.19.1
 scikit-learn==1.3.2
-openpyxl==3.1.2
-pyarrow==11.0.0
+openpyxl>=3.1.2
+pyarrow>=11.0.0
+aicsimageio>=aicsimageio==4.14.0

{small_fish_gui-1.9.3.dist-info → small_fish_gui-1.10.0.dist-info}/METADATA

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.3
+Version: 1.10.0
 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: Wiki, https://github.com/2Echoes/small_fish_gui/wiki
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
 Author-email: Slimani Floric <floric.slimani@live.com>
 License-File: LICENSE
@@ -10,23 +11,24 @@ Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.8
+Requires-Dist: aicsimageio>=4.14.0
 Requires-Dist: big-fish==0.6.2
 Requires-Dist: cellpose==3.0.7
 Requires-Dist: czifile==2019.7.2
-Requires-Dist: freesimplegui==5.1.1
+Requires-Dist: freesimplegui>=5.1.1
 Requires-Dist: imageio==2.34.0
-Requires-Dist: napari-console==0.0.9
-Requires-Dist: napari-plugin-engine==0.2.0
-Requires-Dist: napari-plugin-manager==0.1.0a2
-Requires-Dist: napari-svg==0.1.10
-Requires-Dist: napari==0.4.19.post1
-Requires-Dist: numpy==1.24.4
+Requires-Dist: napari-console>=0.0.9
+Requires-Dist: napari-plugin-engine>=0.2.0
+Requires-Dist: napari-plugin-manager>=0.1.0a2
+Requires-Dist: napari-svg>=0.1.10
+Requires-Dist: napari>=0.4.19.post1
+Requires-Dist: numpy>=1.24.4
 Requires-Dist: openpyxl==3.1.2
-Requires-Dist: pandas==1.5.3
+Requires-Dist: pandas>=1.5.3
 Requires-Dist: pyarrow==11.0.0
 Requires-Dist: scikit-image==0.19.1
 Requires-Dist: scikit-learn==1.3.2
-Requires-Dist: scipy==1.9.1
+Requires-Dist: scipy>=1.9.1
 Description-Content-Type: text/markdown
 
 # Small Fish

small_fish_gui-1.10.0.dist-info/RECORD

@@ -0,0 +1,49 @@
+small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui/README.md,sha256=SFXhmWiISVrOd_cBUodAYaHhMPeKBXyVoPe-fiBxuBw,4671
+small_fish_gui/__init__.py,sha256=FQ99kPNleb90KdywZ4bt2NiizCwyfooTZhndH5O_no8,2050
+small_fish_gui/__main__.py,sha256=mgO_BmBGBsp8steg_lcwCPZ7QzgjgeScL8Npgs1D9Pk,1643
+small_fish_gui/hints.py,sha256=57pO8WA_PymBm5QyXCgYxnZIqqt86B-hO_s_6sv8b5s,1962
+small_fish_gui/requirements.txt,sha256=udO54grAFrmnEqUQC4rDeUMaIyBz3hYB1LJtu1ld7tg,354
+small_fish_gui/utils.py,sha256=LM6QW2ono_LIRv7JXIIq7ZxxbDXqBtZ5uR9gjKJfwM8,1903
+small_fish_gui/.github/workflows/python-publish.yml,sha256=5Ltnuhw9TevhzndlBmdUgYMnS73xEAxSyd1u8DHdn5s,1084
+small_fish_gui/batch/__init__.py,sha256=ku2_Yate-UG89Q0BmE2B9kFV4kOz-u9Lf2lj6VsdFXs,127
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