Merge pull request #341 from RichieHakim/dev

Dev
RichieHakim · Oct 25, 2024 · 72fee2c · 72fee2c
2 parents 567b94b + 2face89
commit 72fee2c
Show file tree

Hide file tree

Showing 14 changed files with 236 additions and 48 deletions.
diff --git a/README.md b/README.md
@@ -48,60 +48,39 @@ With ROICaT, you can:
     <img src="docs/media/umap_with_labels.png" alt="ROICaT" width="300"  align="right"  style="margin-left: 20px"/>
 </div>
 
-Listed below, we have a suite of tools for running the ROICaT pipelines. 
-#### First time users:
-Try it out using the online app or our Google CoLab notebooks below which can be
-run fully remotely without installing anything on your computer.
-#### Normal usage:
-We recommend using our Jupyter notebooks or command line interface which can be
-run locally on any computer.
-
 ### TRACKING: 
 - [Online App](https://huggingface.co/spaces/richiehakim/ROICaT_tracking): Good for first time users. Try it out without installing anything.
 - [Interactive
-  notebook](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/jupyter/tracking/1_tracking_interactive_notebook.ipynb)
-- [Google
-  CoLab](https://githubtocolab.com/RichieHakim/ROICaT/blob/main/notebooks/colab/tracking/1_tracking_interactive_notebook.ipynb) (not up to date)
+  notebook](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/tracking/1_tracking_interactive_notebook.ipynb). Or run on google colab: <a target="_blank" href="https://githubtocolab.com/RichieHakim/ROICaT/blob/main/notebooks/tracking/1_tracking_interactive_notebook.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
 - [Command line interface script](https://github.com/RichieHakim/ROICaT/blob/main/scripts/run_tracking.sh): 
 ```shell
 roicat --pipeline tracking --path_params /path/to/params.yaml --dir_data /folder/with/data/ --dir_save /folder/save/ --prefix_name_save expName --verbose
 ```
 
 ### CLASSIFICATION:
 - [Interactive notebook -
-  Drawing](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/jupyter/classification/A1_classify_by_drawingSelection.ipynb)
-- [Google CoLab -
-  Drawing](https://githubtocolab.com/RichieHakim/ROICaT/blob/main/notebooks/colab/classification/A1_classify_by_drawingSelection_colab.ipynb) (not up to date)
+  Drawing](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/classification/A1_classify_by_drawingSelection.ipynb). Or run on google colab: <a target="_blank" href="https://githubtocolab.com/RichieHakim/ROICaT/blob/main/notebooks/classification/A1_classify_by_drawingSelection.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
 - [Interactive notebook -
-  Labeling](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/jupyter/classification/B1_labeling_interactive.ipynb)
+  Labeling](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/classification/B1_labeling_interactive.ipynb)
 - [Interactive notebook - Train
-  classifier](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/jupyter/classification/B2_classifier_train_interactive.ipynb)
+  classifier](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/classification/B2_classifier_train_interactive.ipynb)
 - [Interactive notebook - Inference with
-  classifier](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/jupyter/classification/B3_classifier_inference_interactive.ipynb)
+  classifier](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/classification/B3_classifier_inference_interactive.ipynb)
 
 **OTHER:** 
 - [Custom data importing
-  notebook](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/jupyter/other/demo_data_importing.ipynb)
+  notebook](https://github.com/RichieHakim/ROICaT/blob/main/notebooks/other/demo_data_importing.ipynb)
 - Use the API to integrate ROICaT functions into your own code:
   [Documentation](https://roicat.readthedocs.io/en/latest/roicat.html).
-- Run the full tracking pipeline using `roicat.pipelines.pipeline_tracking` with
-  default parameters generated from `roicat.util.get_default_paramaters()`.
+- Run the full tracking pipeline using the CLI or
+  `roicat.pipelines.pipeline_tracking` with default parameters generated from
+  `roicat.util.get_default_paramaters()` saved as a yaml file.
 <!-- - Train a new ROInet model using the provided Jupyter Notebook [TODO: link]. -->
 
-# General workflow:
-- **Pass ROIs through ROInet:** Images of the ROIs are passed through a neural
-  network which outputs a feature vector for each image describing what the ROI
-  looks like.
--  **Classification:** The feature vectors can then be used to classify ROIs:
-   - A simple regression-like classifier can be trained using user-supplied
-     labeled data (e.g. an array of images of ROIs and a corresponding array of
-     labels for each ROI).
-   - Alternatively, classification can be done by projecting the feature vectors
-     into a lower-dimensional space using UMAP and then simply circling the
-     region of space to classify the ROIs.
--  **Tracking**: The feature vectors can be combined with information about the
-   position of the ROIs to track the ROIs across imaging sessions/planes.
-
 
 # Installation
 ROICaT works on Windows, MacOS, and Linux. If you have any issues during the
@@ -157,6 +136,21 @@ git pull
 ```
 
 
+# General workflow:
+- **Pass ROIs through ROInet:** Images of the ROIs are passed through a neural
+  network which outputs a feature vector for each image describing what the ROI
+  looks like.
+-  **Classification:** The feature vectors can then be used to classify ROIs:
+   - A simple regression-like classifier can be trained using user-supplied
+     labeled data (e.g. an array of images of ROIs and a corresponding array of
+     labels for each ROI).
+   - Alternatively, classification can be done by projecting the feature vectors
+     into a lower-dimensional space using UMAP and then simply circling the
+     region of space to classify the ROIs.
+-  **Tracking**: The feature vectors can be combined with information about the
+   position of the ROIs to track the ROIs across imaging sessions/planes.
+
+
 # TODO:
 #### algorithmic improvements:
 - [ ] Add in method to use more similarity metrics for tracking
@@ -175,7 +169,7 @@ git pull
 - [x] Make a GUI
 - [ ] Finish ROIextractors integration
 - [ ] Make a Docker container
-- [ ] Make colab demo notebook not require user data
+- ~~Make colab demo notebook not require user data~~
 - [x] Make a better CLI
 #### other:
 - [ ] Write the paper

diff --git a/...ion/A1_classify_by_drawingSelection.ipynb → ...ion/A1_classify_by_drawingSelection.ipynb b/...ion/A1_classify_by_drawingSelection.ipynb → ...ion/A1_classify_by_drawingSelection.ipynb
@@ -26,6 +26,86 @@
     "6. **Save** results\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "5895c4ec",
+   "metadata": {},
+   "source": [
+    "##### If running on google colab:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "876d3c2d",
+   "metadata": {},
+   "source": [
+    "- install roicat\n",
+    "\n",
+    "After running the cell below, the runtime will restart."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0ad98a5a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#@title Install `roicat` if on colab\n",
+    "using_colab = 'google.colab' in str(get_ipython())\n",
+    "\n",
+    "if using_colab:\n",
+    "    !pip uninstall -y tensorflow\n",
+    "    !pip install roicat[classification]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3481e943",
+   "metadata": {},
+   "source": [
+    "- mount google drive"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e148bc5e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#@title mount gdrive if on colab\n",
+    "#@markdown Upload your data to Google Drive, then mount the drive and access the cloud directory here.\n",
+    "#@markdown You can use the sidebar to the left to browse your google drive directories.\n",
+    "\n",
+    "using_colab = 'google.colab' in str(get_ipython())\n",
+    "\n",
+    "if using_colab:\n",
+    "    from google.colab import drive\n",
+    "    path_gdrive = '/content/gdrive'\n",
+    "    drive.mount(path_gdrive, force_remount=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e26b82b7",
+   "metadata": {},
+   "source": [
+    "- enable widgets"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "820c2b9a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if using_colab:\n",
+    "    from google.colab import output\n",
+    "    output.enable_custom_widget_manager()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "c4a1f6ef-7075-4cc3-a046-dd170bb957b9",

diff --git a/...ssification/B1_labeling_interactive.ipynb → ...ssification/B1_labeling_interactive.ipynb b/...ssification/B1_labeling_interactive.ipynb → ...ssification/B1_labeling_interactive.ipynb
diff --git a/...ion/B2_classifier_train_interactive.ipynb → ...ion/B2_classifier_train_interactive.ipynb b/...ion/B2_classifier_train_interactive.ipynb → ...ion/B2_classifier_train_interactive.ipynb
diff --git a/...B3_classifier_inference_interactive.ipynb → ...B3_classifier_inference_interactive.ipynb b/...B3_classifier_inference_interactive.ipynb → ...B3_classifier_inference_interactive.ipynb
diff --git a/notebooks/colab/classification/classify_by_drawingSelection_colab.ipynb b/notebooks/colab/classification/classify_by_drawingSelection_colab.ipynb
diff --git a/notebooks/colab/tracking/tracking_interactive_notebook.ipynb b/notebooks/colab/tracking/tracking_interactive_notebook.ipynb
diff --git a/notebooks/colab/tracking/tracking_visualize_results.ipynb b/notebooks/colab/tracking/tracking_visualize_results.ipynb
diff --git a/...s/jupyter/other/demo_data_importing.ipynb → notebooks/other/demo_data_importing.ipynb b/...s/jupyter/other/demo_data_importing.ipynb → notebooks/other/demo_data_importing.ipynb
diff --git a/...ing/1_tracking_interactive_notebook.ipynb → ...ing/1_tracking_interactive_notebook.ipynb b/...ing/1_tracking_interactive_notebook.ipynb → ...ing/1_tracking_interactive_notebook.ipynb
@@ -28,26 +28,131 @@
   },
   {
    "cell_type": "markdown",
-   "id": "50622a4e",
+   "id": "ba945b86",
    "metadata": {},
    "source": [
-    "# Import libraries"
+    "##### If running on google colab:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "900d6343",
+   "metadata": {},
+   "source": [
+    "- install roicat\n",
+    "\n",
+    "After running the cell below, the runtime will restart."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "c2e99d36",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#@title Install `roicat` if on colab\n",
+    "using_colab = 'google.colab' in str(get_ipython())\n",
+    "\n",
+    "if using_colab:\n",
+    "    !pip uninstall -y tensorflow\n",
+    "    !pip install roicat[tracking]"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "e9824970",
+   "id": "222a013b",
    "metadata": {},
    "source": [
-    "Widen the notebook"
+    "- mount google drive"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "997af9bd",
+   "id": "9793b4fc",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "#@title mount gdrive if on colab\n",
+    "#@markdown Upload your data to Google Drive, then mount the drive and access the cloud directory here.\n",
+    "#@markdown You can use the sidebar to the left to browse your google drive directories.\n",
+    "\n",
+    "using_colab = 'google.colab' in str(get_ipython())\n",
+    "\n",
+    "if using_colab:\n",
+    "    from google.colab import drive\n",
+    "    path_gdrive = '/content/gdrive'\n",
+    "    drive.mount(path_gdrive, force_remount=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f280a589",
+   "metadata": {},
+   "source": [
+    "- enable widgets"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b221ee1b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if using_colab:\n",
+    "    from google.colab import output\n",
+    "    output.enable_custom_widget_manager()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "50622a4e",
+   "metadata": {},
+   "source": [
+    "# Import libraries"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b9293d82",
+   "metadata": {},
+   "source": [
+    "widen the notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "d5c53190",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<style>.container {width:95% !important; }</style>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<style>:root { --jp-notebook-max-width: 100% !important; }</style>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "# widen jupyter notebook window\n",
     "from IPython.display import display, HTML\n",
@@ -65,7 +170,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 20,
    "id": "c4eb1fa5",
    "metadata": {},
    "outputs": [],
@@ -87,10 +192,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "id": "db7f4f25",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/media/rich/OS/Users/Richard/Linux_stuff_on_OS/conda_envs/envs/roicat/lib/python3.11/site-packages/kornia/feature/lightglue.py:44: FutureWarning: `torch.cuda.amp.custom_fwd(args...)` is deprecated. Please use `torch.amp.custom_fwd(args..., device_type='cuda')` instead.\n",
+      "  @torch.cuda.amp.custom_fwd(cast_inputs=torch.float32)\n"
+     ]
+    }
+   ],
    "source": [
     "import roicat"
    ]

diff --git a/...acking/2_tracking_visualize_results.ipynb → ...acking/2_tracking_visualize_results.ipynb b/...acking/2_tracking_visualize_results.ipynb → ...acking/2_tracking_visualize_results.ipynb
diff --git a/...racking/3_tracking_handling_outputs.ipynb → ...racking/3_tracking_handling_outputs.ipynb b/...racking/3_tracking_handling_outputs.ipynb → ...racking/3_tracking_handling_outputs.ipynb
diff --git a/roicat/__init__.py b/roicat/__init__.py
@@ -15,4 +15,4 @@
 
 from .__main__ import run_pipeline
 
-__version__ = '1.4.3'
+__version__ = '1.4.4'
diff --git a/roicat/tracking/alignment.py b/roicat/tracking/alignment.py
@@ -12,7 +12,6 @@
 import torch
 from tqdm.auto import tqdm
 import cv2
-import kornia
 import matplotlib.pyplot as plt
 
 from .. import helpers, util
@@ -1709,6 +1708,8 @@ def __init__(
         device: str = 'cpu',
         verbose: bool = False,
     ):
+        import kornia
+
         super().__init__(device=device, verbose=verbose)
         self.verbose = verbose
 
@@ -2203,6 +2204,8 @@ def __init__(
         device: str = 'cpu',
         verbose: bool = False,
     ):
+        import kornia
+
         super().__init__(device=device, verbose=verbose)
         self.verbose = verbose
         self.threshold_confidence = threshold_confidence
Original file line number	Diff line number	Diff line change
Expand Up		@@ -15,4 +15,4 @@

		from .__main__ import run_pipeline

		__version__ = '1.4.3'
		__version__ = '1.4.4'