small-fish-gui 2.0.2__py3-none-any.whl → 2.1.0__py3-none-any.whl

small_fish_gui/gui/testing.ipynb

@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -40,18 +40,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "image/png": 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",
-      "text/plain": [
-       "<Figure size 640x480 with 1 Axes>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
+     "ename": "NameError",
+     "evalue": "name 'show_spots' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mNameError\u001b[39m                                 Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[1]\u001b[39m\u001b[32m, line 18\u001b[39m\n\u001b[32m     16\u001b[39m spot_image = image.copy()\n\u001b[32m     17\u001b[39m spot_image[\u001b[38;5;28mtuple\u001b[39m(\u001b[38;5;28mlist\u001b[39m(\u001b[38;5;28mzip\u001b[39m(*spots)))] = \u001b[32m255\u001b[39m\n\u001b[32m---> \u001b[39m\u001b[32m18\u001b[39m \u001b[43mshow_spots\u001b[49m([spot_image])\n",
+      "\u001b[31mNameError\u001b[39m: name 'show_spots' is not defined"
+     ]
     }
    ],
    "source": [
@@ -84,7 +85,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -115,7 +116,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -163,7 +164,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -193,7 +194,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -228,7 +229,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -254,7 +255,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -273,7 +274,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -304,7 +305,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -321,7 +322,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -347,7 +348,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -411,7 +412,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -498,7 +499,213 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": []
+   "source": [
+    "# Updating segmentation layout"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import FreeSimpleGUI as sg"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cytoplasm_segmentation_3D = True\n",
+    "nucleus_segmentation_3D = True\n",
+    "is_3D_stack=True"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def _segmentation_layout(\n",
+    "        ) :\n",
+    "    \n",
+    "    layout = []\n",
+    "\n",
+    "    key_2D = \"cyto_radio_2D\"\n",
+    "    options_2D = list()\n",
+    "    key_3D = \"cyto_radio_3D\"\n",
+    "    options_3D = list()\n",
+    "                        \n",
+    "    cyto_radio_2D_seg = sg.Radio(\"2D segmentation\", group_id=1, default=((not cytoplasm_segmentation_3D) or (not is_3D_stack)) or (not is_3D_stack), visible = True, enable_events=True, key=key_2D)\n",
+    "    cyto_radio_max_proj = sg.Radio(\"max proj\", group_id=2, default=False, visible = True)\n",
+    "    cyto_radio_mean_proj = sg.Radio(\"mean proj\", group_id=2, default=True, visible = True)\n",
+    "    cyto_radio_slice_proj = sg.Radio(\"select slice\", group_id=2, default=False, visible = True)\n",
+    "    cyto_int_slice_proj = sg.Spin(list(range(999)), size= (5,1), visible = True, disabled=False)\n",
+    "\n",
+    "    options_2D += [cyto_radio_2D_seg, cyto_radio_max_proj, cyto_radio_mean_proj, cyto_radio_slice_proj, cyto_int_slice_proj]\n",
+    "\n",
+    "    layout += [\n",
+    "            [cyto_radio_2D_seg],\n",
+    "            [cyto_radio_max_proj, cyto_radio_mean_proj, cyto_radio_slice_proj, cyto_int_slice_proj]\n",
+    "            ]\n",
+    "\n",
+    "    if is_3D_stack : \n",
+    "        cyto_radio_3D_seg = sg.Radio(\"3D segmentation\", group_id=1, default=cytoplasm_segmentation_3D, visible = True,enable_events=True, key=key_3D)\n",
+    "        layout += [[cyto_radio_3D_seg]]\n",
+    "\n",
+    "        options_3D += []\n",
+    "    \n",
+    "    layout += [[sg.Button(\"Ok\")]]\n",
+    "                \n",
+    "    #Reference dict\n",
+    "    event_dict = {\n",
+    "        key_2D : options_2D,\n",
+    "        key_3D : options_3D,\n",
+    "    }\n",
+    "\n",
+    "    return layout, event_dict"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "layout,_dict = _segmentation_layout()\n",
+    "window = sg.Window('small fish', layout=layout, margins=(10,10), size=(1000,1000), resizable=False, location=None, enable_close_attempted_event=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "while True :\n",
+    "    try :\n",
+    "        event, values = window.read(timeout=300, timeout_key=\"timeout\")\n",
+    "\n",
+    "        if event == sg.WIN_CLOSE_ATTEMPTED_EVENT or event is None:\n",
+    "            window.close()\n",
+    "            break\n",
+    "        elif event == \"Ok\" :\n",
+    "            window.close()\n",
+    "            break\n",
+    "\n",
+    "        elif event == \"cyto_radio_3D\" :\n",
+    "            for elmnt in ['cyto_radio_max_proj', 'cyto_radio_mean_proj','cyto_radio_slice_proj','cyto_int_slice_proj'] :\n",
+    "                print(_dict[elmnt])\n",
+    "                _dict[elmnt].update(disabled=True)\n",
+    "        elif event == \"cyto_radio_2D\" :\n",
+    "            for elmnt in ['cyto_radio_max_proj', 'cyto_radio_mean_proj','cyto_radio_slice_proj','cyto_int_slice_proj'] :\n",
+    "                _dict[elmnt].update(disabled=False)\n",
+    "\n",
+    "        elif event != \"timeout\" :\n",
+    "            print(event)\n",
+    "    \n",
+    "    except Exception as e :\n",
+    "        window.close()\n",
+    "        raise(e)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Testint custom events on Napari"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os, platform\n",
+    "import napari\n",
+    "\n",
+    "system_type = platform.system()\n",
+    "\n",
+    "\n",
+    "if system_type == \"Linux\" :\n",
+    "  try :\n",
+    "    os.environ[\"QT_QPA_PLATFORM\"] = \"xcb\"\n",
+    "  except Exception :\n",
+    "    pass\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from napari.layers import Labels, Points, Image\n",
+    "from napari.utils.events import Event, EmitterGroup\n",
+    "from magicgui import magicgui\n",
+    "from magicgui.widgets import SpinBox, Container\n",
+    "\n",
+    "class MyWidgetCreator :\n",
+    "    def __init__(self) :\n",
+    "        self.events = EmitterGroup(source=self, coucou_event = None)\n",
+    "        self.widget = self.create_widget()\n",
+    "\n",
+    "    def create_widget(self) :\n",
+    "\n",
+    "        @magicgui(\n",
+    "            call_button=\"coucou\"\n",
+    "        )\n",
+    "        def event_emitter(name: str) :\n",
+    "            print(\"Coucou !!\")\n",
+    "            self.events.coucou_event(name=name)\n",
+    "        return event_emitter\n",
+    "\n",
+    "\n",
+    "class PresenceCounter :\n",
+    "    def __init__(self) :\n",
+    "        self.value = 0\n",
+    "    \n",
+    "    def _on_salutation(self, event) :\n",
+    "        self.value += 1\n",
+    "        print(f\"{event.name} arrived! We are {self.value} now!\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Coucou !!\n",
+      "F arrived! We are 1 now!\n",
+      "Coucou !!\n",
+      "R arrived! We are 2 now!\n",
+      "Coucou !!\n",
+      "R arrived! We are 3 now!\n",
+      "Coucou !!\n",
+      "D arrived! We are 4 now!\n",
+      "Coucou !!\n",
+      "G arrived! We are 5 now!\n"
+     ]
+    }
+   ],
+   "source": [
+    "Viewer = napari.Viewer()\n",
+    "my_widget = MyWidgetCreator()\n",
+    "presence_counter = PresenceCounter()\n",
+    "\n",
+    "my_widget.events.coucou_event.connect(presence_counter._on_salutation)\n",
+    "Viewer.window.add_dock_widget(my_widget.widget, name='test')\n",
+    "\n",
+    "napari.run()"
+   ]
   },
   {
    "cell_type": "code",
@@ -510,7 +717,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "dev",
+   "display_name": "small_fish_3.12",
    "language": "python",
    "name": "python3"
   },
@@ -524,7 +731,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.21"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

small_fish_gui/gui/tooltips.py

@@ -12,4 +12,10 @@ FLOW_THRESHOLD_TOOLTIP = """ (float) from 0. to 1.
 The flow_threshold parameter is the maximum allowed error of the flows for each mask. 
 Increase this threshold if cellpose is not returning as many ROIs as you’d expect. 
 Similarly, decrease this threshold if cellpose is returning too many ill-shaped ROIs.
-""" #Cellpose 4.0.6 doc
+""" #Cellpose 4.0.6 doc
+
+MIN_SIZE_TOOLTIP = """ (int) >0 ; pixel
+Default to 15px. Minimum size for predicted regions during cytoplasm or nucleus segmentation. Smaller regions will be discarded.
+"""
+
+REMOVE_BACKGROUND_TOOLTIP = """RANSAC fit + substraction method is applied using selected channel as background and detection channel as signal. \nResulting signal is passed for spot detection and quantification but NOT for segmentation."""

small_fish_gui/hints.py

@@ -2,6 +2,7 @@
 #Add keys hinting to user_parameters instance keys.
 
 from typing import TypedDict, Tuple
+from dataclasses import dataclass
 from numpy import ndarray
     
 class pipeline_parameters(TypedDict) :
@@ -11,23 +12,31 @@ class pipeline_parameters(TypedDict) :
             alpha : float
             anisotropy : float
             beta : float
+            background_max_trial : int
             channel_to_compute : int
-            cellprob_threshold_cyto : float
-            cellprob_threshold_nuc : float
+            cytoplasm_cellprob_threshold : float
+            background_channel : int
             cytoplasm_segmentation_3D : bool
             cluster_size : int
-            cyto_model_name : str
+            cytoplasm_model_name : str
             cytoplasm_diameter : int
             cytoplasm_channel : int
+            cytoplasm_min_size : int
+            cytoplasm_max_proj : bool
+            cytoplasm_mean_proj : bool
+            cytoplasm_select_slice : bool
+            cytoplasm_selected_slice : int
             do_cluster_computation : bool
+            do_background_removal : bool
             do_dense_regions_deconvolution : bool
             do_spots_excel : bool
             do_spots_feather : bool
             do_spots_csv : bool
+            do_background_removal : bool
             dim : int
             filename : str
-            flow_threshold_cyto : int
-            flow_threshold_nuc : int
+            cytoplasm_flow_threshold : int
+            nucleus_flow_threshold : int
             gamma : float
             image_path : str
             image : ndarray
@@ -42,17 +51,25 @@ class pipeline_parameters(TypedDict) :
             minimum_distance_z : float
             is_3D_stack : bool
             is_multichannel : bool
+            nucleus_cellprob_threshold : float
             nucleus_channel_signal : int
             nucleus_segmentation_3D : bool
             nucleus_diameter : int
             nucleus_model_name : str
             nucleus_channel : int
+            nucleus_min_size : int
+            nucleus_max_proj : bool
+            nucleus_mean_proj : bool
+            nucleus_select_slice : bool
+            nucleus_selected_slice : int
             other_nucleus_image : str
             reordered_shape : Tuple[int,int,int,int,int]
             do_segmentation : bool
             shape : Tuple[int,int,int,int,int]
-            save_segmentation_visual : bool
+            save_segmentation_visuals : bool
+            segment_only_nuclei : bool
             segmentation_done : bool
+            seg_control_saving_path : str
             show_interactive_threshold_selector : bool
             spots_extraction_folder : str
             spots_filename : str
@@ -60,7 +77,6 @@ class pipeline_parameters(TypedDict) :
             spot_size_x : int
             spot_size_y : int
             spot_size_z : int
-            segment_only_nuclei : bool
             cytoplasm_segmentation_3D : bool
             nucleus_segmentation_3D : bool
             show_napari_corrector : bool

small_fish_gui/interface/__init__.py

@@ -8,4 +8,10 @@ from .image import check_format
 from .image import FormatError
 from .image import get_voxel_size
 
-from .inoutput import write_results
+from .inoutput import write_results
+
+from .user_settings import (SettingsDict,
+                            get_settings,
+                            get_default_settings,
+                            write_settings
+                            )

small_fish_gui/interface/default_settings.py

@@ -0,0 +1,118 @@
+""""
+Constant submodule to have a common reference for parameters default values
+"""
+import os
+
+WORKING_DIRECTORY = None
+
+#Image
+IS_MULTICHANNEL = False
+IS_3D_STACK = False
+CHANNEL = 0
+NUC_CHANNEL = 1
+
+#Segmentation
+FLOW_THRESHOLD = 0.4
+CELLPROB_THRESHOD = 0.
+CYTO_MODEL = "cpsam"
+NUC_MODEL = "cpsam"
+CYTOPLASM_DIAMETER = 90
+NUC_DIAMETER = 60
+ANISOTROPY = 1. 
+SHOW_SEGMENTATION = True
+SEGMENT_ONLY_NUCLEI = False
+DO_3D_SEMGENTATION = False
+VISUAL_PATH = os.getcwd()
+SAVE_SEGMENTATION_VISUAL = False
+NUCLEUS_MIN_SIZE = 15
+CYTOPLASM_MIN_SIZE = 15
+CYTOPLASM_max_proj = False
+CYTOPLASM_mean_proj = True
+CYTOPLASM_select_slice = False
+CYTOPLASM_selected_slice = 0
+
+NUCLEUS_MIN_SIZE = 15
+NUCLEUS_max_proj = False
+NUCLEUS_mean_proj = True
+NUCLEUS_select_slice = False
+NUCLEUS_selected_slice = 0
+
+#Detection
+THRESHOLD = None
+THRESHOLD_PENALTY = 1
+DO_DENSE_REGIONS_DECONVOLUTION = False
+DO_CLUSTER_COMPUTATION = False
+DO_CLUSTER_COMPUTATION = False
+SHOW_NAPARI_CORRECTOR = True
+INTERACTIVE_THRESHOLD = False
+VOXEL_SIZE = (1,2,3)
+
+#Background removal
+DO_BACKGROUND_REMOVAL = False
+BACKGROUND_CHANNEL = 0
+
+#Deconvolution
+ALPHA = 0.5
+BETA = 1.
+GAMMA = 3.
+
+#Clustering
+CLUSTER_SIZE = 400
+MIN_NUMBER_SPOTS = 5
+
+#Coloc
+COLOC_RANGE = 400
+
+#Spots Extraction
+DO_CSV = False
+DO_EXCEL = False
+SPOT_EXTRACTION_FOLDER = os.getcwd()
+
+
+def get_default_settings() :
+    return {
+        "working_directory" : os.getcwd() if WORKING_DIRECTORY is None else WORKING_DIRECTORY,
+        "do_background_removal" : DO_BACKGROUND_REMOVAL,
+        "background_channel" : BACKGROUND_CHANNEL,
+        "multichannel_stack" : IS_MULTICHANNEL,
+        "stack_3D" : IS_3D_STACK,
+        "detection_channel" : CHANNEL,
+        "nucleus_channel" : NUC_CHANNEL,
+        "flow_threshold" : FLOW_THRESHOLD,
+        "cellprob_threshold" : CELLPROB_THRESHOD,
+        "cytoplasm_diameter" : CYTOPLASM_DIAMETER,
+        "nucleus_diameter" : NUC_DIAMETER,
+        "anisotropy" : ANISOTROPY,
+        "cytoplasm_model" : CYTO_MODEL,
+        "nucleus_model" : NUC_MODEL,
+        "show_segmentation" : SHOW_SEGMENTATION,
+        "segment_only_nuclei" : SEGMENT_ONLY_NUCLEI,
+        "do_3D_segmentation" : DO_3D_SEMGENTATION,
+        "save_segmentation_visuals" : SAVE_SEGMENTATION_VISUAL,
+        "threshold" : THRESHOLD,
+        "threshold_penalty" : THRESHOLD_PENALTY,
+        "do_dense_regions_deconvolution" : DO_DENSE_REGIONS_DECONVOLUTION,
+        "do_cluster" : DO_CLUSTER_COMPUTATION,
+        "show_napari_corrector" : SHOW_NAPARI_CORRECTOR,
+        "interactive_threshold_selector" : INTERACTIVE_THRESHOLD,
+        "alpha" : ALPHA,
+        "beta" : BETA,
+        "gamma" : GAMMA,
+        "cluster_size" : CLUSTER_SIZE ,
+        "min_spot" : MIN_NUMBER_SPOTS,
+        "coloc_range" : COLOC_RANGE,
+        "do_csv" : DO_CSV,
+        "do_excel" : DO_EXCEL,
+        "spot_extraction_folder" : SPOT_EXTRACTION_FOLDER,
+        "voxel_size" : VOXEL_SIZE,
+        "nucleus_min_size" : NUCLEUS_MIN_SIZE,
+        "cytoplasm_min_size" : CYTOPLASM_MIN_SIZE,
+        "cytoplasm_max_proj" : CYTOPLASM_max_proj,
+        "cytoplasm_mean_proj" : CYTOPLASM_mean_proj,
+        "cytoplasm_select_slice" : CYTOPLASM_select_slice,
+        "cytoplasm_selected_slice" : CYTOPLASM_selected_slice,
+        "nucleus_max_proj" : NUCLEUS_max_proj,
+        "nucleus_mean_proj" : NUCLEUS_mean_proj,
+        "nucleus_select_slice" : NUCLEUS_select_slice,
+        "nucleus_selected_slice" : NUCLEUS_selected_slice,
+    }

small_fish_gui/interface/image.py

@@ -1,8 +1,9 @@
+import re
+import tifffile
 from bigfish.stack import read_image
 from czifile import imread
+from czifile import CziFile
 from ..utils import check_parameter
-import re
-from aicsimageio import AICSImage
 from typing import Optional, Tuple
 
 class FormatError(Exception):
@@ -43,17 +44,48 @@ def get_voxel_size(filepath: str) -> Optional[Tuple[Optional[float], Optional[fl
     """
     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
+    /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)
+        if filepath.endswith('.czi'):
+            with CziFile(filepath) as czi:
+                metadata = czi.metadata()  # returns XML metadata
+                # try to parse voxel sizes from XML
+                import xml.etree.ElementTree as ET
+                root = ET.fromstring(metadata)
+                scaling_distance = root.findall('.//Scaling//Items//Distance//Value')
+                if len(scaling_distance) in [2,3] :
+                    for scale in scaling_distance :
+                        res = [float(scale.text) * 1e9 for scale in scaling_distance] #m to nm
+                    res.reverse()
+                    return tuple(res)
+                else :
+                    raise Exception("Couln't find voxel size on xml metadata")
+
+        elif filepath.endswith(('.tif', '.tiff')):
+            with tifffile.TiffFile(filepath) as tif:
+                ij_meta = tif.imagej_metadata
+                page = tif.pages[0]  # first image page
+                # X/Y resolution as (numerator, denominator)
+                xres = page.tags['XResolution'].value
+                yres = page.tags['YResolution'].value
+                # ResolutionUnit: must be 'nm' for this calculation
+                res_unit = ij_meta.get("unit")
+
+                if res_unit and str(res_unit) != 'nm':
+                    xy_size = 1 / (xres[0] / xres[1]) * 1e3 #um to nm
+                elif res_unit and str(res_unit) != 'NONE':
+                    xy_size = 1 / (xres[0] / xres[1]) #um to nm
+                else:
+                    xy_size = None
+
+                # Z spacing from ImageJ metadata
+                if res_unit and str(res_unit) != 'nm':
+                    z_size = ij_meta.get('spacing', None) * 1e3 
+                else :
+                    z_size = ij_meta.get('spacing', None)
+
+                return (z_size,xy_size, xy_size )
     except Exception as e:
         print(f"Failed to read voxel size from {filepath}: {e}")
         return None