spacr 0.3.68__tar.gz → 0.3.70__tar.gz

{spacr-0.3.68/spacr.egg-info → spacr-0.3.70}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.68
+Version: 0.3.70
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

spacr-0.3.70/notebooks/old/.ipynb_checkpoints/Untitled1-checkpoint.ipynb

@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

spacr-0.3.70/notebooks/old/.ipynb_checkpoints/trade_2025-checkpoint.ipynb

@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

spacr-0.3.70/notebooks/old/Untitled1.ipynb

@@ -0,0 +1,230 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "40424f6c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import json\n",
+    "import cv2\n",
+    "import numpy as np\n",
+    "import openai\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "\n",
+    "\n",
+    "def prepare_data_for_finetuning(image_folder, test_size=0.2, output_file=\"fine_tune_dataset.jsonl\"):\n",
+    "    \"\"\"\n",
+    "    Prepares a dataset for fine-tuning GPT-4 using grayscale images and corresponding masks.\n",
+    "\n",
+    "    Args:\n",
+    "        image_folder (str): Path to the folder containing grayscale images and a \"masks\" subfolder.\n",
+    "        test_size (float): Proportion of the dataset to include in the test split.\n",
+    "        output_file (str): Output JSONL file for fine-tuning.\n",
+    "    \n",
+    "    Returns:\n",
+    "        tuple: Paths to the training and testing datasets in JSONL format.\n",
+    "    \"\"\"\n",
+    "    def convert_to_16bit(image):\n",
+    "        \"\"\"\n",
+    "        Converts an image to 16-bit format.\n",
+    "        \"\"\"\n",
+    "        if image.dtype == np.uint8:  # Convert 8-bit to 16-bit\n",
+    "            image = cv2.normalize(image, None, 0, 65535, cv2.NORM_MINMAX, dtype=cv2.CV_16U)\n",
+    "        elif image.dtype == np.float32:  # Convert float32 to 16-bit\n",
+    "            image = (image * 65535).clip(0, 65535).astype(np.uint16)\n",
+    "        elif image.dtype != np.uint16:  # Convert other types to 16-bit\n",
+    "            image = cv2.normalize(image, None, 0, 65535, cv2.NORM_MINMAX, dtype=cv2.CV_16U)\n",
+    "        return image\n",
+    "\n",
+    "    images_path = [f for f in os.listdir(image_folder) if os.path.isfile(os.path.join(image_folder, f))]\n",
+    "    masks_folder = os.path.join(image_folder, \"masks\")\n",
+    "    data = []\n",
+    "\n",
+    "    for image_file in images_path:\n",
+    "        image_path = os.path.join(image_folder, image_file)\n",
+    "        mask_path = os.path.join(masks_folder, image_file)\n",
+    "        \n",
+    "        if not os.path.exists(mask_path):\n",
+    "            continue  # Skip if mask does not exist\n",
+    "        \n",
+    "        # Load image and mask\n",
+    "        image = cv2.imread(image_path, cv2.IMREAD_UNCHANGED)\n",
+    "        mask = cv2.imread(mask_path, cv2.IMREAD_UNCHANGED)\n",
+    "\n",
+    "        # Skip if images fail to load\n",
+    "        if image is None or mask is None:\n",
+    "            print(f\"Skipping {image_file}: Unable to load.\")\n",
+    "            continue\n",
+    "\n",
+    "        # Convert to 16-bit if necessary\n",
+    "        image = convert_to_16bit(image)\n",
+    "        mask = convert_to_16bit(mask)\n",
+    "\n",
+    "        # Create a prompt-response pair\n",
+    "        prompt = f\"Generate a mask for the grayscale image with dimensions {image.shape}.\"\n",
+    "        completion = f\"The mask has been generated with specific contours and intensity ranges.\"\n",
+    "        \n",
+    "        # Append to the dataset\n",
+    "        data.append({\"prompt\": prompt, \"completion\": completion})\n",
+    "\n",
+    "    # Split the data\n",
+    "    train_data, test_data = train_test_split(data, test_size=test_size, random_state=42)\n",
+    "\n",
+    "    # Save the datasets\n",
+    "    train_file = f\"train_{output_file}\"\n",
+    "    test_file = f\"test_{output_file}\"\n",
+    "    \n",
+    "    with open(train_file, \"w\") as train_f:\n",
+    "        for entry in train_data:\n",
+    "            train_f.write(json.dumps(entry) + \"\\n\")\n",
+    "    \n",
+    "    with open(test_file, \"w\") as test_f:\n",
+    "        for entry in test_data:\n",
+    "            test_f.write(json.dumps(entry) + \"\\n\")\n",
+    "\n",
+    "    return train_file, test_file\n",
+    "\n",
+    "\n",
+    "def fine_tune_gpt4(train_file, model=\"gpt-4\", epochs=4, learning_rate=1e-4):\n",
+    "    \"\"\"\n",
+    "    Fine-tunes GPT-4 using the prepared training dataset.\n",
+    "\n",
+    "    Args:\n",
+    "        train_file (str): Path to the training dataset in JSONL format.\n",
+    "        model (str): Base GPT-4 model to fine-tune.\n",
+    "        epochs (int): Number of epochs for fine-tuning.\n",
+    "        learning_rate (float): Learning rate for fine-tuning.\n",
+    "    \n",
+    "    Returns:\n",
+    "        str: Fine-tuned model ID.\n",
+    "    \"\"\"\n",
+    "    openai.api_key = os.getenv(\"OPENAI_API_KEY\")\n",
+    "\n",
+    "    # Upload the training file\n",
+    "    print(\"Uploading training file...\")\n",
+    "    try:\n",
+    "        with open(train_file, \"rb\") as f:\n",
+    "            response = openai.File.create(file=f, purpose=\"fine-tune\")\n",
+    "        training_file_id = response[\"id\"]\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error uploading training file: {e}\")\n",
+    "        return None\n",
+    "\n",
+    "    # Fine-tune the model\n",
+    "    print(\"Starting fine-tuning...\")\n",
+    "    try:\n",
+    "        fine_tune_response = openai.FineTune.create(\n",
+    "            model=model,\n",
+    "            training_file=training_file_id,\n",
+    "            n_epochs=epochs,\n",
+    "            learning_rate=learning_rate\n",
+    "        )\n",
+    "        fine_tune_id = fine_tune_response[\"id\"]\n",
+    "        print(f\"Fine-tuning initiated with ID: {fine_tune_id}\")\n",
+    "        return fine_tune_id\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error during fine-tuning: {e}\")\n",
+    "        return None\n",
+    "\n",
+    "\n",
+    "def save_fine_tuned_model(fine_tune_id, output_model_path):\n",
+    "    \"\"\"\n",
+    "    Saves the fine-tuned model to disk.\n",
+    "\n",
+    "    Args:\n",
+    "        fine_tune_id (str): The fine-tune ID returned after training.\n",
+    "        output_model_path (str): Path to save the fine-tuned model.\n",
+    "    \"\"\"\n",
+    "    try:\n",
+    "        fine_tune_details = openai.FineTune.retrieve(id=fine_tune_id)\n",
+    "        fine_tuned_model = fine_tune_details[\"fine_tuned_model\"]\n",
+    "        \n",
+    "        with open(output_model_path, \"w\") as f:\n",
+    "            f.write(fine_tuned_model)\n",
+    "        print(f\"Fine-tuned model saved to: {output_model_path}\")\n",
+    "    except Exception as e:\n",
+    "        print(f\"Error saving fine-tuned model: {e}\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "1cbc2b20",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Uploading training file...\n",
+      "Error uploading training file: \n",
+      "\n",
+      "You tried to access openai.File, but this is no longer supported in openai>=1.0.0 - see the README at https://github.com/openai/openai-python for the API.\n",
+      "\n",
+      "You can run `openai migrate` to automatically upgrade your codebase to use the 1.0.0 interface. \n",
+      "\n",
+      "Alternatively, you can pin your installation to the old version, e.g. `pip install openai==0.28`\n",
+      "\n",
+      "A detailed migration guide is available here: https://github.com/openai/openai-python/discussions/742\n",
+      "\n",
+      "Error saving fine-tuned model: \n",
+      "\n",
+      "You tried to access openai.FineTune, but this is no longer supported in openai>=1.0.0 - see the README at https://github.com/openai/openai-python for the API.\n",
+      "\n",
+      "You can run `openai migrate` to automatically upgrade your codebase to use the 1.0.0 interface. \n",
+      "\n",
+      "Alternatively, you can pin your installation to the old version, e.g. `pip install openai==0.28`\n",
+      "\n",
+      "A detailed migration guide is available here: https://github.com/openai/openai-python/discussions/742\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "image_folder = '/nas_mnt/carruthers/Einar/dsred/train'\n",
+    "test_size=0.1\n",
+    "\n",
+    "# Step 1: Prepare data\n",
+    "train_file, test_file = prepare_data_for_finetuning(image_folder)\n",
+    "\n",
+    "# Step 2: Fine-tune GPT-4\n",
+    "fine_tune_id = fine_tune_gpt4(train_file, epochs=3, learning_rate=5e-5)\n",
+    "\n",
+    "# Step 3: Save the fine-tuned model\n",
+    "save_fine_tuned_model(fine_tune_id, \"./fine_tuned_gpt4_mask_generator.txt\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7ac25b4a",
+   "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-0.3.70/notebooks/old/trade_2025.ipynb

@@ -0,0 +1,230 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "e7243b46",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import alpaca_trade_api as tradeapi\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "from datetime import datetime, timedelta\n",
+    "from sklearn.ensemble import RandomForestRegressor\n",
+    "from sklearn.metrics import mean_squared_error\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "class StockTrader:\n",
+    "    def __init__(self, alpaca_api_key, alpaca_secret_key, base_url='https://paper-api.alpaca.markets'):\n",
+    "        # Initialize Alpaca API\n",
+    "        self.api = tradeapi.REST(alpaca_api_key, alpaca_secret_key, base_url, api_version='v2')\n",
+    "        self.model = None\n",
+    "        self.test_mode = False\n",
+    "\n",
+    "    def fetch_historical_data(self, symbol, start_date, end_date):\n",
+    "        # Fetch historical daily bars\n",
+    "        bars = self.api.get_bars(\n",
+    "            symbol,\n",
+    "            '1Day',\n",
+    "            start=start_date.isoformat(),\n",
+    "            end=end_date.isoformat()\n",
+    "        ).df\n",
+    "        bars = bars[bars['symbol'] == symbol]\n",
+    "        return bars\n",
+    "\n",
+    "    def prepare_features(self, data):\n",
+    "        # Prepare features for the model\n",
+    "        data['return'] = data['close'].pct_change()\n",
+    "        data['volatility'] = data['close'].rolling(window=5).std()\n",
+    "        data['momentum'] = data['close'] / data['close'].shift(5) - 1\n",
+    "        data['ma5'] = data['close'].rolling(window=5).mean()\n",
+    "        data['ma10'] = data['close'].rolling(window=10).mean()\n",
+    "        data['ma_ratio'] = data['ma5'] / data['ma10']\n",
+    "        data = data.dropna()\n",
+    "        features = data[['return', 'volatility', 'momentum', 'ma_ratio']]\n",
+    "        return features\n",
+    "\n",
+    "    def train_model(self, symbol, start_date, end_date):\n",
+    "        # Fetch and prepare data\n",
+    "        data = self.fetch_historical_data(symbol, start_date, end_date)\n",
+    "        features = self.prepare_features(data)\n",
+    "        target = data['close'].shift(-1).dropna()\n",
+    "        features = features.iloc[:-1]  # Align features and target\n",
+    "\n",
+    "        # Split into training and testing sets\n",
+    "        split_index = int(len(features) * 0.8)\n",
+    "        X_train, X_test = features[:split_index], features[split_index:]\n",
+    "        y_train, y_test = target[:split_index], target[split_index:]\n",
+    "\n",
+    "        # Train the model\n",
+    "        self.model = RandomForestRegressor(n_estimators=100, random_state=42)\n",
+    "        self.model.fit(X_train, y_train)\n",
+    "\n",
+    "        # Evaluate the model\n",
+    "        y_pred = self.model.predict(X_test)\n",
+    "        mse = mean_squared_error(y_test, y_pred)\n",
+    "        print(f\"Model trained. Test MSE: {mse:.4f}\")\n",
+    "\n",
+    "        if self.test_mode:\n",
+    "            self.backtest_strategy(X_test, y_test, y_pred)\n",
+    "\n",
+    "    def backtest_strategy(self, X_test, y_test, y_pred):\n",
+    "        # Simulate trading strategy based on predictions\n",
+    "        initial_capital = 100000\n",
+    "        positions = pd.DataFrame(index=X_test.index).fillna(0.0)\n",
+    "        positions['signal'] = np.where(y_pred > X_test['return'], 1, -1)\n",
+    "        positions['holdings'] = positions['signal'] * y_test\n",
+    "\n",
+    "        portfolio = positions['holdings'].cumsum() * 100  # Assuming 100 shares per trade\n",
+    "        portfolio += initial_capital\n",
+    "\n",
+    "        # Plot the portfolio value over time\n",
+    "        plt.figure(figsize=(10, 5))\n",
+    "        plt.plot(portfolio)\n",
+    "        plt.title('Backtested Portfolio Value')\n",
+    "        plt.xlabel('Date')\n",
+    "        plt.ylabel('Portfolio Value ($)')\n",
+    "        plt.show()\n",
+    "\n",
+    "        total_return = (portfolio.iloc[-1] - initial_capital) / initial_capital * 100\n",
+    "        print(f\"Total return from backtesting: {total_return:.2f}%\")\n",
+    "\n",
+    "    def predict(self, symbol):\n",
+    "        # Predict the next day's closing price\n",
+    "        end_date = datetime.now()\n",
+    "        start_date = end_date - timedelta(days=60)  # Get recent data for features\n",
+    "        data = self.fetch_historical_data(symbol, start_date, end_date)\n",
+    "        features = self.prepare_features(data)\n",
+    "\n",
+    "        if features.empty:\n",
+    "            print(\"Not enough data to make a prediction.\")\n",
+    "            return\n",
+    "\n",
+    "        latest_features = features.iloc[-1].values.reshape(1, -1)\n",
+    "        predicted_price = self.model.predict(latest_features)[0]\n",
+    "        current_price = data['close'].iloc[-1]\n",
+    "        expected_return = (predicted_price - current_price) / current_price * 100\n",
+    "\n",
+    "        print(f\"Predicted next closing price for {symbol}: ${predicted_price:.2f}\")\n",
+    "        print(f\"Expected return: {expected_return:.2f}%\")\n",
+    "\n",
+    "        return expected_return\n",
+    "\n",
+    "    def execute_trade(self, symbol, expected_return, risk_tolerance=0.05):\n",
+    "        # Decide whether to buy or sell based on expected return\n",
+    "        if expected_return > risk_tolerance:\n",
+    "            # Place a buy order\n",
+    "            try:\n",
+    "                self.api.submit_order(\n",
+    "                    symbol=symbol,\n",
+    "                    qty=10,  # Number of shares to buy\n",
+    "                    side='buy',\n",
+    "                    type='market',\n",
+    "                    time_in_force='day'\n",
+    "                )\n",
+    "                print(f\"Placed a market buy order for {symbol}\")\n",
+    "            except Exception as e:\n",
+    "                print(f\"Error placing buy order: {e}\")\n",
+    "        elif expected_return < -risk_tolerance:\n",
+    "            # Place a sell order\n",
+    "            try:\n",
+    "                self.api.submit_order(\n",
+    "                    symbol=symbol,\n",
+    "                    qty=10,  # Number of shares to sell\n",
+    "                    side='sell',\n",
+    "                    type='market',\n",
+    "                    time_in_force='day'\n",
+    "                )\n",
+    "                print(f\"Placed a market sell order for {symbol}\")\n",
+    "            except Exception as e:\n",
+    "                print(f\"Error placing sell order: {e}\")\n",
+    "        else:\n",
+    "            print(f\"No trade executed for {symbol}. Expected return does not meet risk tolerance.\")\n",
+    "\n",
+    "    def run(self, symbol, test_mode=False):\n",
+    "        self.test_mode = test_mode\n",
+    "        start_date = datetime.now() - timedelta(days=365*2)\n",
+    "        end_date = datetime.now() - timedelta(days=1)\n",
+    "\n",
+    "        # Train the model\n",
+    "        self.train_model(symbol, start_date, end_date)\n",
+    "\n",
+    "        if not self.test_mode:\n",
+    "            # Predict and trade\n",
+    "            expected_return = self.predict(symbol)\n",
+    "            if expected_return is not None:\n",
+    "                self.execute_trade(symbol, expected_return)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "29ebde4b",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "APIError",
+     "evalue": "Invalid format for parameter start: error parsing '2022-12-03T13:32:03.137224' as RFC3339 or 2006-01-02 time: parsing time \"2022-12-03T13:32:03.137224\": extra text: \"T13:32:03.137224\"",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAPIError\u001b[0m                                  Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 7\u001b[0m\n\u001b[1;32m      5\u001b[0m trader \u001b[38;5;241m=\u001b[39m StockTrader(alpaca_api_key, alpaca_secret_key)\n\u001b[1;32m      6\u001b[0m \u001b[38;5;66;03m# To backtest the model\u001b[39;00m\n\u001b[0;32m----> 7\u001b[0m \u001b[43mtrader\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mAAPL\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtest_mode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m      8\u001b[0m \u001b[38;5;66;03m# To predict and trade on current data\u001b[39;00m\n\u001b[1;32m      9\u001b[0m trader\u001b[38;5;241m.\u001b[39mrun(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mAAPL\u001b[39m\u001b[38;5;124m'\u001b[39m, test_mode\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m)\n",
+      "Cell \u001b[0;32mIn[2], line 142\u001b[0m, in \u001b[0;36mStockTrader.run\u001b[0;34m(self, symbol, test_mode)\u001b[0m\n\u001b[1;32m    139\u001b[0m end_date \u001b[38;5;241m=\u001b[39m datetime\u001b[38;5;241m.\u001b[39mnow() \u001b[38;5;241m-\u001b[39m timedelta(days\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m)\n\u001b[1;32m    141\u001b[0m \u001b[38;5;66;03m# Train the model\u001b[39;00m\n\u001b[0;32m--> 142\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtrain_model\u001b[49m\u001b[43m(\u001b[49m\u001b[43msymbol\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstart_date\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mend_date\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    144\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtest_mode:\n\u001b[1;32m    145\u001b[0m     \u001b[38;5;66;03m# Predict and trade\u001b[39;00m\n\u001b[1;32m    146\u001b[0m     expected_return \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpredict(symbol)\n",
+      "Cell \u001b[0;32mIn[2], line 41\u001b[0m, in \u001b[0;36mStockTrader.train_model\u001b[0;34m(self, symbol, start_date, end_date)\u001b[0m\n\u001b[1;32m     39\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mtrain_model\u001b[39m(\u001b[38;5;28mself\u001b[39m, symbol, start_date, end_date):\n\u001b[1;32m     40\u001b[0m     \u001b[38;5;66;03m# Fetch and prepare data\u001b[39;00m\n\u001b[0;32m---> 41\u001b[0m     data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfetch_historical_data\u001b[49m\u001b[43m(\u001b[49m\u001b[43msymbol\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstart_date\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mend_date\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     42\u001b[0m     features \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprepare_features(data)\n\u001b[1;32m     43\u001b[0m     target \u001b[38;5;241m=\u001b[39m data[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mclose\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m.\u001b[39mshift(\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m)\u001b[38;5;241m.\u001b[39mdropna()\n",
+      "Cell \u001b[0;32mIn[2], line 18\u001b[0m, in \u001b[0;36mStockTrader.fetch_historical_data\u001b[0;34m(self, symbol, start_date, end_date)\u001b[0m\n\u001b[1;32m     16\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mfetch_historical_data\u001b[39m(\u001b[38;5;28mself\u001b[39m, symbol, start_date, end_date):\n\u001b[1;32m     17\u001b[0m     \u001b[38;5;66;03m# Fetch historical daily bars\u001b[39;00m\n\u001b[0;32m---> 18\u001b[0m     bars \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mapi\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_bars\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m     19\u001b[0m \u001b[43m        \u001b[49m\u001b[43msymbol\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     20\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m1Day\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m     21\u001b[0m \u001b[43m        \u001b[49m\u001b[43mstart\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstart_date\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43misoformat\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     22\u001b[0m \u001b[43m        \u001b[49m\u001b[43mend\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mend_date\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43misoformat\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     23\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mdf\n\u001b[1;32m     24\u001b[0m     bars \u001b[38;5;241m=\u001b[39m bars[bars[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msymbol\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m==\u001b[39m symbol]\n\u001b[1;32m     25\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m bars\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:735\u001b[0m, in \u001b[0;36mREST.get_bars\u001b[0;34m(self, symbol, timeframe, start, end, adjustment, limit, feed, asof, sort)\u001b[0m\n\u001b[1;32m    724\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget_bars\u001b[39m(\u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m    725\u001b[0m              symbol: Union[\u001b[38;5;28mstr\u001b[39m, List[\u001b[38;5;28mstr\u001b[39m]],\n\u001b[1;32m    726\u001b[0m              timeframe: TimeFrame,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    733\u001b[0m              sort: Optional[Sort] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m    734\u001b[0m              ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m BarsV2:\n\u001b[0;32m--> 735\u001b[0m     bars \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mlist\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_bars_iter\u001b[49m\u001b[43m(\u001b[49m\u001b[43msymbol\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    736\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43mtimeframe\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    737\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43mstart\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    738\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43mend\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    739\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43madjustment\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    740\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43mlimit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    741\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43mfeed\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfeed\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    742\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43masof\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43masof\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    743\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43msort\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msort\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    744\u001b[0m \u001b[43m                                   \u001b[49m\u001b[43mraw\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    745\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m BarsV2(bars)\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:718\u001b[0m, in \u001b[0;36mREST.get_bars_iter\u001b[0;34m(self, symbol, timeframe, start, end, adjustment, limit, feed, asof, sort, raw)\u001b[0m\n\u001b[1;32m    697\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget_bars_iter\u001b[39m(\u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m    698\u001b[0m                   symbol: Union[\u001b[38;5;28mstr\u001b[39m, List[\u001b[38;5;28mstr\u001b[39m]],\n\u001b[1;32m    699\u001b[0m                   timeframe: TimeFrame,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    706\u001b[0m                   sort: Optional[Sort] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m    707\u001b[0m                   raw\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m BarIterator:\n\u001b[1;32m    708\u001b[0m     bars \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_data_get(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mbars\u001b[39m\u001b[38;5;124m'\u001b[39m, symbol,\n\u001b[1;32m    709\u001b[0m                           timeframe\u001b[38;5;241m=\u001b[39mtimeframe,\n\u001b[1;32m    710\u001b[0m                           adjustment\u001b[38;5;241m=\u001b[39madjustment,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    716\u001b[0m                           sort\u001b[38;5;241m=\u001b[39msort,\n\u001b[1;32m    717\u001b[0m                           )\n\u001b[0;32m--> 718\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m bar \u001b[38;5;129;01min\u001b[39;00m bars:\n\u001b[1;32m    719\u001b[0m         \u001b[38;5;28;01mif\u001b[39;00m raw:\n\u001b[1;32m    720\u001b[0m             \u001b[38;5;28;01myield\u001b[39;00m bar\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:594\u001b[0m, in \u001b[0;36mREST._data_get\u001b[0;34m(self, endpoint, symbol_or_symbols, api_version, endpoint_base, resp_grouped_by_symbol, page_limit, feed, asof, loc, **kwargs)\u001b[0m\n\u001b[1;32m    592\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m endpoint:\n\u001b[1;32m    593\u001b[0m     path \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mendpoint\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m--> 594\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdata_get\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfeed\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfeed\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    595\u001b[0m \u001b[43m                     \u001b[49m\u001b[43mapi_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mapi_version\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    596\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m resp_grouped_by_symbol:\n\u001b[1;32m    597\u001b[0m     k \u001b[38;5;241m=\u001b[39m endpoint \u001b[38;5;129;01mor\u001b[39;00m endpoint_base\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:274\u001b[0m, in \u001b[0;36mREST.data_get\u001b[0;34m(self, path, data, feed, api_version)\u001b[0m\n\u001b[1;32m    272\u001b[0m     data \u001b[38;5;241m=\u001b[39m data \u001b[38;5;129;01mor\u001b[39;00m {}\n\u001b[1;32m    273\u001b[0m     data[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfeed\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m feed\n\u001b[0;32m--> 274\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    275\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mGET\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbase_url\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbase_url\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mapi_version\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mapi_version\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    276\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:222\u001b[0m, in \u001b[0;36mREST._request\u001b[0;34m(self, method, path, data, base_url, api_version)\u001b[0m\n\u001b[1;32m    220\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m    221\u001b[0m     \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 222\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_one_request\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mopts\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mretry\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    223\u001b[0m     \u001b[38;5;28;01mexcept\u001b[39;00m RetryException:\n\u001b[1;32m    224\u001b[0m         retry_wait \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_retry_wait\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:248\u001b[0m, in \u001b[0;36mREST._one_request\u001b[0;34m(self, method, url, opts, retry)\u001b[0m\n\u001b[1;32m    246\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m resp\u001b[38;5;241m.\u001b[39mstatus_code \u001b[38;5;129;01min\u001b[39;00m retry_codes \u001b[38;5;129;01mand\u001b[39;00m retry \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m    247\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m RetryException()\n\u001b[0;32m--> 248\u001b[0m     \u001b[43mraise_api_error\u001b[49m\u001b[43m(\u001b[49m\u001b[43mresp\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mhttp_error\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    249\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m resp\u001b[38;5;241m.\u001b[39mtext \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m    250\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m resp\u001b[38;5;241m.\u001b[39mjson()\n",
+      "File \u001b[0;32m~/anaconda3/envs/spacr/lib/python3.9/site-packages/alpaca_trade_api/rest.py:83\u001b[0m, in \u001b[0;36mraise_api_error\u001b[0;34m(resp, http_error)\u001b[0m\n\u001b[1;32m     81\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m http_error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m     82\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmessage\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01min\u001b[39;00m error:\n\u001b[0;32m---> 83\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m APIError(error, http_error) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m     84\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m http_error \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n",
+      "\u001b[0;31mAPIError\u001b[0m: Invalid format for parameter start: error parsing '2022-12-03T13:32:03.137224' as RFC3339 or 2006-01-02 time: parsing time \"2022-12-03T13:32:03.137224\": extra text: \"T13:32:03.137224\""
+     ]
+    }
+   ],
+   "source": [
+    "if __name__ == '__main__':\n",
+    "    alpaca_api_key = 'PKJATKYKR4NWCYALKL58'\n",
+    "    alpaca_secret_key = '8aFRppO0HdabLAO8b05ZImUwSd0bEmv4hqpU0Hqs'\n",
+    "\n",
+    "    trader = StockTrader(alpaca_api_key, alpaca_secret_key)\n",
+    "    # To backtest the model\n",
+    "    trader.run('AAPL', test_mode=True)\n",
+    "    # To predict and trade on current data\n",
+    "    trader.run('AAPL', test_mode=False)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "77a1c83f",
+   "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-0.3.70/settings/measure_crop_settings.csv

@@ -0,0 +1,48 @@
+Key,Value
+src,D:\20240920-IRE1a-inhibitors_20240920_132333\plate1\test\merged
+verbose,False
+experiment,exp
+test_mode,False
+test_nr,10
+channels,"[0, 1, 2, 3]"
+save_measurements,True
+radial_dist,True
+calculate_correlation,True
+manders_thresholds,"[15, 85, 95]"
+homogeneity,True
+homogeneity_distances,"[8, 16, 32]"
+save_arrays,False
+save_png,True
+use_bounding_box,False
+png_size,"[[224, 224]]"
+png_dims,"[0, 1, 2]"
+normalize,False
+normalize_by,png
+crop_mode,cell
+dialate_pngs,False
+dialate_png_ratios,"[1, 10]"
+timelapse,False
+timelapse_objects,cell
+plot,False
+n_jobs,6
+cell_mask_dim,4
+nucleus_mask_dim,5
+pathogen_mask_dim,6
+cytoplasm,True
+uninfected,False
+cell_min_size,8000
+nucleus_min_size,2000
+pathogen_min_size,500
+cytoplasm_min_size,0
+merge_edge_pathogen_cells,True
+Paths,
+General,
+Cell,
+Nucleus,
+Pathogen,
+Measurements,
+Object Image,
+Plot,
+Test,
+Timelapse,
+Advanced,

{spacr-0.3.68 → spacr-0.3.70}/setup.py

@@ -69,7 +69,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.3.68",
+    version="0.3.70",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.3.68 → spacr-0.3.70}/spacr/ml.py

@@ -1493,27 +1493,32 @@ def _calculate_similarity(df, features, col_to_compare, val1, val2):
         # Add a small value to the diagonal elements for regularization
         epsilon = 1e-5
         inv_cov_matrix = np.linalg.inv(cov_matrix + np.eye(cov_matrix.shape[0]) * epsilon)
-    
+        
     # Calculate similarity scores
-    df['similarity_to_pos_euclidean'] = df[features].apply(lambda row: euclidean(row, pos_control), axis=1)
-    df['similarity_to_neg_euclidean'] = df[features].apply(lambda row: euclidean(row, neg_control), axis=1)
-    df['similarity_to_pos_cosine'] = df[features].apply(lambda row: cosine(row, pos_control), axis=1)
-    df['similarity_to_neg_cosine'] = df[features].apply(lambda row: cosine(row, neg_control), axis=1)
-    df['similarity_to_pos_mahalanobis'] = df[features].apply(lambda row: mahalanobis(row, pos_control, inv_cov_matrix), axis=1)
-    df['similarity_to_neg_mahalanobis'] = df[features].apply(lambda row: mahalanobis(row, neg_control, inv_cov_matrix), axis=1)
-    df['similarity_to_pos_manhattan'] = df[features].apply(lambda row: cityblock(row, pos_control), axis=1)
-    df['similarity_to_neg_manhattan'] = df[features].apply(lambda row: cityblock(row, neg_control), axis=1)
-    df['similarity_to_pos_minkowski'] = df[features].apply(lambda row: minkowski(row, pos_control, p=3), axis=1)
-    df['similarity_to_neg_minkowski'] = df[features].apply(lambda row: minkowski(row, neg_control, p=3), axis=1)
-    df['similarity_to_pos_chebyshev'] = df[features].apply(lambda row: chebyshev(row, pos_control), axis=1)
-    df['similarity_to_neg_chebyshev'] = df[features].apply(lambda row: chebyshev(row, neg_control), axis=1)
-    df['similarity_to_pos_hamming'] = df[features].apply(lambda row: hamming(row, pos_control), axis=1)
-    df['similarity_to_neg_hamming'] = df[features].apply(lambda row: hamming(row, neg_control), axis=1)
-    df['similarity_to_pos_jaccard'] = df[features].apply(lambda row: jaccard(row, pos_control), axis=1)
-    df['similarity_to_neg_jaccard'] = df[features].apply(lambda row: jaccard(row, neg_control), axis=1)
-    df['similarity_to_pos_braycurtis'] = df[features].apply(lambda row: braycurtis(row, pos_control), axis=1)
-    df['similarity_to_neg_braycurtis'] = df[features].apply(lambda row: braycurtis(row, neg_control), axis=1)
-    
+    def safe_similarity(func, row, control):
+        try:
+            return func(row, control)
+        except Exception:
+            return np.nan
+        
+    # Calculate similarity scores
+    try:
+        df['similarity_to_pos_euclidean'] = df[features].apply(lambda row: safe_similarity(euclidean, row, pos_control), axis=1)
+        df['similarity_to_neg_euclidean'] = df[features].apply(lambda row: safe_similarity(euclidean, row, neg_control), axis=1)
+        df['similarity_to_pos_cosine'] = df[features].apply(lambda row: safe_similarity(cosine, row, pos_control), axis=1)
+        df['similarity_to_neg_cosine'] = df[features].apply(lambda row: safe_similarity(cosine, row, neg_control), axis=1)
+        df['similarity_to_pos_mahalanobis'] = df[features].apply(lambda row: safe_similarity(mahalanobis, row, pos_control, inv_cov_matrix), axis=1)
+        df['similarity_to_neg_mahalanobis'] = df[features].apply(lambda row: safe_similarity(mahalanobis, row, neg_control, inv_cov_matrix), axis=1)
+        df['similarity_to_pos_manhattan'] = df[features].apply(lambda row: safe_similarity(cityblock, row, pos_control), axis=1)
+        df['similarity_to_neg_manhattan'] = df[features].apply(lambda row: safe_similarity(cityblock, row, neg_control), axis=1)
+        df['similarity_to_pos_minkowski'] = df[features].apply(lambda row: safe_similarity(minkowski, row, pos_control, p=3), axis=1)
+        df['similarity_to_neg_minkowski'] = df[features].apply(lambda row: safe_similarity(minkowski, row, neg_control, p=3), axis=1)
+        df['similarity_to_pos_chebyshev'] = df[features].apply(lambda row: safe_similarity(chebyshev, row, pos_control), axis=1)
+        df['similarity_to_neg_chebyshev'] = df[features].apply(lambda row: safe_similarity(chebyshev, row, neg_control), axis=1)
+        df['similarity_to_pos_braycurtis'] = df[features].apply(lambda row: safe_similarity(braycurtis, row, pos_control), axis=1)
+        df['similarity_to_neg_braycurtis'] = df[features].apply(lambda row: safe_similarity(braycurtis, row, neg_control), axis=1)
+    except Exception as e:
+        print(f"Error calculating similarity scores: {e}")    
     return df
 
 def interperate_vision_model(settings={}):

{spacr-0.3.68 → spacr-0.3.70/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.68
+Version: 0.3.70
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson