spacr 0.3.52__tar.gz → 0.3.60__tar.gz

{spacr-0.3.52/spacr.egg-info → spacr-0.3.60}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.52
+Version: 0.3.60
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

spacr-0.3.60/notebooks/spacr_computer_vision.ipynb

@@ -0,0 +1,150 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "335dcd14",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "# use this cell to generate train and test folders: datasets/train/nc and pc and datasets/test/nc and pc\n",
+    "from spacr.io import generate_training_dataset\n",
+    "\n",
+    "settings = {'src':'path', # (path) path to source folder (where origional images were stored)\n",
+    "            'dataset_mode':'annotation', # (string) annotation, measurement, metadata\n",
+    "            'tables':['cell'],# (list of strings) The tabels present in the database, excluding png_list\n",
+    "            'test_split':0.1, # (float) Fraction of images used for the test set\n",
+    "            'annotation_column':'test', # (Optional, string) If using mode annotation, The annotation column in the database\n",
+    "            'annotated_classes':[1], # (Optional, list of integers) If using mode annotation, The interger in annotation_column, if len(annotated_classes) is 1, class 2 will be generated from a random selection of images.\n",
+    "            'metadata_type_by':'column_name', # (Optional, strin) If using mode medatada, If using mode medatada,the column class_metadata elements are in\n",
+    "            'class_metadata':[['c15'],['c19']], # (Optional, list of lists of strings) If using mode medatada, the elements that deffine each class \n",
+    "            'png_type':'cell_png', # (Optional, string) string in the path of each image (used to filter images)\n",
+    "            'nuclei_limit':False, # (Optional, bool) if cell and nucleus in tables, filter for number of nuclei per cell\n",
+    "            'pathogen_limit':0, # (Optional, integer) if cell and pathogen in tables, filter for number of pathogen per cell\n",
+    "            'uninfected':True, # (Optional, bool) if cell and pathogen in tables, bool for uninfected cells (cells)\n",
+    "            'size':None # (Optional, integer or NoneType) limit for number of images to include in total (test + train) per class\n",
+    "           }\n",
+    "\n",
+    "generate_training_dataset(settings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b4431164",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# train a torch model\n",
+    "from spacr.deep_spacr import train_test_model\n",
+    "\n",
+    "settings = {'src':'path', # (path) path to source folder (ends with datasets/training)\n",
+    "            'train':True, # (bool) - Train\n",
+    "            'test': False, # (bool) - Test\n",
+    "            'custom_model':False, # (path) - path to a custom model\n",
+    "            'classes':['nc','pc'], # (list) - list of classes (folder names in dataset/training/train or test)\n",
+    "            'model_type':'maxvit_t', # (string) - Name of torch model architecture\n",
+    "            'optimizer_type':'adamw', # (string) - type of optimizer\n",
+    "            'schedule':'reduce_lr_on_plateau', # (string) - type of scheduler (reduce_lr_on_plateau or step_lr)\n",
+    "            'loss_type':'focal_loss', # (string) - Loss function (binary_cross_entropy_with_logits or focal_loss)\n",
+    "            'normalize':True, # (bool) - Apply ImageNet normalization to images before training.\n",
+    "            'image_size':224, # (int) - Size of images, height and width.\n",
+    "            'batch_size':64, # (int) - Nr. of images per batch\n",
+    "            'epochs':10, # (int) - Nr. of epochs for training\n",
+    "            'val_split':0.1, # (float) - Fraction of images in validation dataset\n",
+    "            'learning_rate':0.0001, # (float) - Learning rate per epoch\n",
+    "            'weight_decay':0.00001, # (float) - Fraction of random weights decay (regularization)\n",
+    "            'dropout_rate':0.1, # (float) - Fraction of weights to omit per epoch (regularization)\n",
+    "            'init_weights':True, # (bool) - Initiate model with ImageNet weights\n",
+    "            'amsgrad':True, # (bool) - guard against exploding gradients\n",
+    "            'use_checkpoint':True, # (bool) - checkpoint gradient calculations to save VRAM at the expence of computation\n",
+    "            'gradient_accumulation':True, # (bool) - Accumulate gradients to mimic larger batches\n",
+    "            'gradient_accumulation_steps':4, # (int) - Epochs to accumulate gradients\n",
+    "            'intermedeate_save':True, # Save intermediate states of the model\n",
+    "            'pin_memory':True, # (bool) - Whether to pin memory for the data loader\n",
+    "            'n_jobs':30, # (int) - Number of threads to use\n",
+    "            'train_channels':['r','g','b'], # (list of 'r', 'g', and/or 'b') - PNG channels to use for training\n",
+    "            'augment':False, # (bool) - Augment the dataset, vertical, horizontal flip and rotate each image to artificially expand the dataset 8 fold.\n",
+    "            'verbose':True}\n",
+    "\n",
+    "train_test_model(settings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5770fb79",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "# generate a tar dataset\n",
+    "\n",
+    "from spacr.io import generate_dataset\n",
+    "\n",
+    "settings = {'src':'path', # (path) path to source folder (where origional images were stored)\n",
+    "           'file_metadata':'cell_png', # (Optional, string) string in the path of each image (used to filter images)\n",
+    "           'experiment':'test', # (string) - Name of dataset\n",
+    "           'sample':10000} # (Optional, integer or NoneType) limit for number of images to include in the dataset\n",
+    "\n",
+    "generate_dataset(settings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "086fcefb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# apply a model to a tar dataset\n",
+    "\n",
+    "from spacr.deep_spacr import apply_model_to_tar\n",
+    "\n",
+    "settings = {'dataset':'path.tar', # (path) - path to tar dataset (ends with .tar) \n",
+    "            'model_path':'path.pth', # (path) - path to model (ends with .pth) \n",
+    "            'file_type':'cell_png', # (Optional, string) string in the path of each image (used to filter images)\n",
+    "            'image_size':224, # (int) - Size of images, height and width\n",
+    "            'batch_size':64, # (int) - Nr. of images per batch\n",
+    "            'normalize':True, # (bool) - Apply ImageNet normalization to images before training.\n",
+    "            'score_threshold':0.5, # (float) - Score to byass the classes\n",
+    "            'n_jobs':30, # (int) - Number of threads to use\n",
+    "            'verbose':True}\n",
+    "\n",
+    "result_df = apply_model_to_tar(settings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "28debecd",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "spacr",
+   "language": "python",
+   "name": "spacr"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.19"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{spacr-0.3.52 → spacr-0.3.60}/setup.py

@@ -69,7 +69,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.3.52",
+    version="0.3.60",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.3.52 → spacr-0.3.60}/spacr/gui_elements.py

@@ -706,7 +706,7 @@ class spacrProgressBar(ttk.Progressbar):
 
     def set_label_position(self):
         if self.label and self.progress_label:
-            row_info = self.grid_info().get('row', 0)
+            row_info = self.grid_info().get('row_name', 0)
             col_info = self.grid_info().get('column', 0)
             col_span = self.grid_info().get('columnspan', 1)
             self.progress_label.grid(row=row_info + 1, column=col_info, columnspan=col_span, pady=5, padx=5, sticky='ew')

{spacr-0.3.52 → spacr-0.3.60}/spacr/gui_utils.py

@@ -106,32 +106,6 @@ def parse_list(value):
     except (ValueError, SyntaxError) as e:
         raise ValueError(f"Invalid format for list: {value}. Error: {e}")
 
-def parse_list_v1(value):
-    """
-    Parses a string representation of a list and returns the parsed list.
-
-    Args:
-        value (str): The string representation of the list.
-
-    Returns:
-        list: The parsed list, which can contain integers, floats, or strings.
-
-    Raises:
-        ValueError: If the input value is not a valid list format or contains mixed types or unsupported types.
-    """
-    try:
-        parsed_value = ast.literal_eval(value)
-        if isinstance(parsed_value, list):
-            # Check if all elements are homogeneous (either all int, float, or str)
-            if all(isinstance(item, (int, float, str)) for item in parsed_value):
-                return parsed_value
-            else:
-                raise ValueError("List contains mixed types or unsupported types")
-        else:
-            raise ValueError(f"Expected a list but got {type(parsed_value).__name__}")
-    except (ValueError, SyntaxError) as e:
-        raise ValueError(f"Invalid format for list: {value}. Error: {e}")
-
 # Usage example in your create_input_field function
 def create_input_field(frame, label_text, row, var_type='entry', options=None, default_value=None):
     """
@@ -696,91 +670,6 @@ def ensure_after_tasks(frame):
     if not hasattr(frame, 'after_tasks'):
         frame.after_tasks = []
 
-def display_gif_in_plot_frame_v1(gif_path, parent_frame):
-    """Display and zoom a GIF to fill the entire parent_frame, maintaining aspect ratio, with lazy resizing and caching."""
-    # Clear parent_frame if it contains any previous widgets
-    for widget in parent_frame.winfo_children():
-        widget.destroy()
-
-    # Load the GIF
-    gif = Image.open(gif_path)
-
-    # Get the aspect ratio of the GIF
-    gif_width, gif_height = gif.size
-    gif_aspect_ratio = gif_width / gif_height
-
-    # Create a label to display the GIF and configure it to fill the parent_frame
-    label = tk.Label(parent_frame, bg="black")
-    label.grid(row=0, column=0, sticky="nsew")  # Expands in all directions (north, south, east, west)
-
-    # Configure parent_frame to stretch the label to fill available space
-    parent_frame.grid_rowconfigure(0, weight=1)
-    parent_frame.grid_columnconfigure(0, weight=1)
-
-    # Cache for storing resized frames (lazily filled)
-    resized_frames_cache = {}
-
-    # Last frame dimensions
-    last_frame_width = 0
-    last_frame_height = 0
-
-    def resize_and_crop_frame(frame_idx, frame_width, frame_height):
-        """Resize and crop the current frame of the GIF to fit the parent_frame while maintaining the aspect ratio."""
-        # If the frame is already cached at the current size, return it
-        if (frame_idx, frame_width, frame_height) in resized_frames_cache:
-            return resized_frames_cache[(frame_idx, frame_width, frame_height)]
-
-        # Calculate the scaling factor to zoom in on the GIF
-        scale_factor = max(frame_width / gif_width, frame_height / gif_height)
-
-        # Calculate new dimensions while maintaining the aspect ratio
-        new_width = int(gif_width * scale_factor)
-        new_height = int(gif_height * scale_factor)
-
-        # Resize the GIF to fit the frame
-        gif.seek(frame_idx)
-        resized_gif = gif.copy().resize((new_width, new_height), Image.Resampling.LANCZOS)
-
-        # Calculate the cropping box to center the resized GIF in the frame
-        crop_left = (new_width - frame_width) // 2
-        crop_top = (new_height - frame_height) // 2
-        crop_right = crop_left + frame_width
-        crop_bottom = crop_top + frame_height
-
-        # Crop the resized GIF to exactly fit the frame
-        cropped_gif = resized_gif.crop((crop_left, crop_top, crop_right, crop_bottom))
-
-        # Convert the cropped frame to a Tkinter-compatible format
-        frame_image = ImageTk.PhotoImage(cropped_gif)
-
-        # Cache the resized frame
-        resized_frames_cache[(frame_idx, frame_width, frame_height)] = frame_image
-
-        return frame_image
-
-    def update_frame(frame_idx):
-        """Update the GIF frame using lazy resizing and caching."""
-        # Get the current size of the parent_frame
-        frame_width = parent_frame.winfo_width()
-        frame_height = parent_frame.winfo_height()
-
-        # Only resize if the frame size has changed
-        nonlocal last_frame_width, last_frame_height
-        if frame_width != last_frame_width or frame_height != last_frame_height:
-            last_frame_width, last_frame_height = frame_width, frame_height
-
-        # Get the resized and cropped frame image
-        frame_image = resize_and_crop_frame(frame_idx, frame_width, frame_height)
-        label.config(image=frame_image)
-        label.image = frame_image  # Keep a reference to avoid garbage collection
-
-        # Move to the next frame, or loop back to the beginning
-        next_frame_idx = (frame_idx + 1) % gif.n_frames
-        parent_frame.after(gif.info['duration'], update_frame, next_frame_idx)
-
-    # Start the GIF animation from frame 0
-    update_frame(0)
-
 def display_gif_in_plot_frame(gif_path, parent_frame):
     """Display and zoom a GIF to fill the entire parent_frame, maintaining aspect ratio, with lazy resizing and caching."""
     # Clear parent_frame if it contains any previous widgets