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add notebook to run timing of some operations
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‎notebooks/EpiCure_Timing.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "9629f8e8-86e7-4a6d-85a6-a6b34d548545",
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"metadata": {},
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"source": [
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"# Time some basic operations in movie with varying sizes\n",
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"\n",
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"Notebook to automatically do time some steps of EpiCure:\n",
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"* **Load the movie and segmentation**\n",
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"* **removing the border cells** \n",
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"* **performs the tracking** (with the default parameters)\n",
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"* **perform some basic editions, repeated several times** \n",
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"\n",
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"*This notebook is part of EpiCure release, see https://github.pasteur.fr/Image-Analysis-Hub/epicure for more informations*"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "47dd0f63-87ef-4dce-8034-413b45e77992",
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"metadata": {},
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"outputs": [],
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"source": [
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"#### Parent directory to process. It will go through all the sub-folders\n",
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"main_path = \"../../../data/timing/\"\n",
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"imgname = main_path+\"Ecad\"\n",
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"skelname = main_path+\"Ecad_skeleton\"\n",
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"#subnames = [\"-subcrop\", \"-crop-crop\", \"-crop\", \"\", \"-subset\", \"-subset-subset\"]\n",
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"subnames = [\"\", \"-subset\", \"-subset-subset\"]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "48bf6960-5798-45e9-8271-de1ece6897a4",
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"metadata": {},
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"outputs": [],
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"source": [
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"import epicure.epicuring as epicure\n",
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"import epicure.Utils as ut\n",
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"import os\n",
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"import time\n",
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"from vispy import keys\n",
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"import sys\n",
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"\n",
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"original_stdout = sys.stdout\n",
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"\n",
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"def doOneMovie( imgname, skelname, subname ):\n",
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" \"\"\" Process one movie: clear (or not) the border cells and performs tracking \"\"\"\n",
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" print( \"EpiCuring movie \"+imgname+subname+\".tif\" )\n",
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" \n",
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" start_time = time.time()\n",
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" sys.stdout = open( os.devnull, 'w' )\n",
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" epic = epicure.EpiCure()\n",
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" epic.verbose = 0 ## Choose the level of printing infos during process (0: minimal to 3: debug informations)\n",
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" ## Loading movie\n",
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" epic.load_movie( imgname+subname+\".tif\" )\n",
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" sys.stdout = original_stdout\n",
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" ctime = time.time()\n",
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" print( f\"Time to load movie: {ctime-start_time}\" )\n",
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" ## Loading segmentation and initialize all\n",
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" start_time = ctime\n",
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" sys.stdout = open( os.devnull, 'w' )\n",
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" epic.go_epicure( \"epics\", skelname+subname+\".tif\" ) ## start EpiCure, load the segmentation, prepare everything\n",
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" sys.stdout = original_stdout\n",
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" ctime = time.time()\n",
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" print( f\"Time to load segmentation and initialize: {ctime-start_time}\" )\n",
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" print( f\"Nb of untracked cells: {epic.nlabels()}\" )\n",
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" ## Remove border cells\n",
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" start_time = ctime \n",
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" sys.stdout = open( os.devnull, 'w' )\n",
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" epic.editing.border_size.setText(\"1\") ## Choose the border size parameter to remove the cells that are within the given distance of the image border\n",
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" epic.editing.remove_border() ## EpiCure option to remove all cells that are touching the image border\n",
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" sys.stdout = original_stdout\n",
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" ctime = time.time()\n",
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" print( f\"Time to remove cells on border: {ctime-start_time}\" )\n",
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" ## Track with LapTrack centroids, no features\n",
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" start_time = ctime\n",
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" sys.stdout = open( os.devnull, 'w' )\n",
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" epic.tracking.do_tracking() ## Performs tracking with the default parameters. If you have saved preferences, it will use it.\n",
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" sys.stdout = original_stdout\n",
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" ctime = time.time()\n",
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" print( f\"Time to track: {ctime-start_time}\" )\n",
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" ## Do some basic editings to measure reactivness\n",
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" start_time = ctime \n",
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" view = epic.viewer.window.qt_viewer\n",
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" for i in range(50):\n",
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" view.canvas.events.key_press(key=keys.Key(\"b\"), modifiers=[])\n",
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" view.canvas.events.key_press(key=keys.Key(\"c\"), modifiers=[])\n",
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" view.canvas.events.key_press(key=keys.Key(\"v\"), modifiers=[])\n",
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" ctime = time.time()\n",
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" print( f\"Time to change view: {ctime-start_time}\" )\n",
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" ## Get neighbor labels\n",
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" start_time = ctime\n",
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" segedit = epic.editing\n",
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" label = epic.seg[0,200,200]\n",
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" graph = ut.get_neighbor_graph( epic.seg[0], distance=3 )\n",
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" neighbors = ut.get_neighbors( label, graph )\n",
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" neigh = neighbors[0]\n",
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" ## Hoping labels are neighbors\n",
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" start_time = ctime\n",
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" segedit = epic.editing\n",
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" sys.stdout = open( os.devnull, 'w' )\n",
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" for i in range(30):\n",
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" segedit.merge_labels( 0, label, neigh )\n",
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" view.canvas.events.key_press(key=keys.Key(\"Z\"), modifiers=[\"Control\"])\n",
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" sys.stdout = original_stdout\n",
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" ctime = time.time()\n",
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" print( f\"Time to merge and cancel: {ctime-start_time}\" )\n",
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" \n",
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" start_time = ctime\n",
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" sys.stdout = open( os.devnull, 'w' )\n",
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" epic.save_epicures() ## save the results in the ouput \"epics\" folder(s)\n",
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" sys.stdout = original_stdout\n",
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" ctime = time.time()\n",
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" print( f\"Time to save the segmentation/epic infos: {ctime-start_time}\" )\n",
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" del epic\n",
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"\n",
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"## be sure to start from scratch\n",
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"if os.path.exists( os.path.join(main_path+\"epics/\") ):\n",
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" import shutil\n",
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" shutil.rmtree(os.path.join(main_path+\"epics/\"))\n",
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"\n",
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"import warnings\n",
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"warnings.filterwarnings(\"ignore\", category=UserWarning)\n",
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"warnings.filterwarnings(\"ignore\", category=FutureWarning)\n",
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"for subname in subnames:\n",
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" doOneMovie( imgname, skelname, subname )"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9e374937-76fe-4f14-94dc-92562bedf397",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "epic",
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"language": "python",
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"name": "epic"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.12"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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