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Merge pull request #143 from RichieHakim/dev
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Dev
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RichieHakim authored Dec 12, 2023
2 parents ac768d1 + 0cc98db commit 82a31c2
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Showing 5 changed files with 15 additions and 76 deletions.
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{
"cells": [
{
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"id": "c6860758-e614-4e0b-b9bb-3cc55af78e9c",
"metadata": {},
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]
},
{
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]
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]
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]
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]
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]
},
{
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"metadata": {},
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]
},
{
"attachments": {},
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"metadata": {},
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]
},
{
"attachments": {},
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"metadata": {},
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"metadata": {},
"outputs": [],
"source": [
"dir_allOuterFolders = r'/media/rich/bigSSD/analysis_data/face_rhythm/mouse_0403L/stat_and_ops'\n",
"dir_allOuterFolders = r'/media/rich/bigSSD/data_raw/BMI/mouse_0921R/'\n",
"\n",
"pathSuffixToStat = 'stat.npy'\n",
"pathSuffixToOps = 'ops.npy'\n",
Expand All @@ -162,7 +153,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
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"metadata": {},
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]
},
{
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Expand All @@ -204,7 +193,6 @@
]
},
{
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"metadata": {},
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]
},
{
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]
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]
},
{
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"metadata": {},
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]
},
{
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"id": "cd9e6c9d-c4aa-4a20-ad15-d0329bbad201",
"metadata": {},
Expand All @@ -321,7 +305,6 @@
]
},
{
"attachments": {},
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]
},
{
"attachments": {},
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"id": "05cb7b22-c206-41e7-b1d6-55e58593f915",
"metadata": {},
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" data=emb,\n",
" idx_images_overlay=idx_images_overlay,\n",
" images_overlay=images_overlay[:, 6:30][:,:,6:30],\n",
" size_images_overlay=0.4,\n",
" size_images_overlay=0.3,\n",
" frac_overlap_allowed=0.5,\n",
" figsize=(1200,1200),\n",
" alpha_points=1.0,\n",
Expand All @@ -383,7 +365,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "ec7e6060-cd39-4666-9a39-e3b540f34562",
"metadata": {},
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]
},
{
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"id": "ec4640cd-047b-4bf3-90f8-6f4d72eda620",
"metadata": {},
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" cmap=roicat.helpers.simple_cmap([[1,0,0],[0,1,0]]),\n",
")\n",
"\n",
"roicat.visualization.display_toggle_image_stack(FOVs_colored,)"
"roicat.visualization.display_toggle_image_stack(\n",
" FOVs_colored,\n",
" image_size=(FOVs_colored[0].shape[0]*2, FOVs_colored[0].shape[1]*2)\n",
")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "53667b6f-0bb0-4738-8878-754998be0a55",
"metadata": {},
Expand All @@ -485,17 +467,16 @@
"metadata": {},
"outputs": [],
"source": [
"dir_save = r'/media/rich/bigSSD/analysis_data/face_rhythm/mouse_0403L/'\n",
"filename_save = 'mouse_0403L'\n",
"dir_save = r'/media/rich/bigSSD/analysis_data/BMI/day0_stuff/mouse_0921R'\n",
"filename_save = 'mouse_0921R'\n",
"\n",
"path_save = str(Path(dir_save).resolve() / (filename_save + '.ROICaT.classification_drawn.results' + '.pkl'))\n",
"print(f'path_save: {path_save}')\n",
"\n",
"roicat.helpers.pickle_save(classification_output, path_save)"
"roicat.helpers.pickle_save(classification_output, path_save, mkdir=True)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "d3a77d9f-a95c-4533-9df7-07f105595630",
"metadata": {},
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