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‎pyRASP_Example_ImageFolderAnalysis.ipynb

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"metadata": {},
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"outputs": [
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{
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"ename": "TypeError",
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"evalue": "Series.sum() got an unexpected keyword argument 'axis'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[2], line 29\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;124;03m\"\"\" the command below will run the analyse_images analysis:\u001b[39;00m\n\u001b[1;32m 2\u001b[0m \n\u001b[1;32m 3\u001b[0m \u001b[38;5;124;03m folder (string): Folder containing images\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[38;5;124;03mAll have defaults except folder, which is necessary.\u001b[39;00m\n\u001b[1;32m 23\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 25\u001b[0m folder \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mabspath(\n\u001b[1;32m 26\u001b[0m \u001b[38;5;124mr\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexample_images\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 27\u001b[0m ) \u001b[38;5;66;03m# example file, replace as you wish. Always input as the absolute path of a raw string\u001b[39;00m\n\u001b[0;32m---> 29\u001b[0m \u001b[43mRASP\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43manalyse_images\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfolder\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mprotein_string\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mC1\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mthres\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m0.05\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlarge_thres\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m500.\u001b[39;49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m~/Documents/Dropbox/Cambridge University Dropbox/Joseph Beckwith/Chemistry/Lee/Code/Python/pyRASP/src/RASPRoutines.py:666\u001b[0m, in \u001b[0;36mRASP_Routines.analyse_images\u001b[0;34m(self, folder, imtype, thres, large_thres, gsigma, rwave, protein_string, cell_string, if_filter, im_start, cell_analysis, one_savefile, disp, folder_recursive, error_reduction)\u001b[0m\n\u001b[1;32m 664\u001b[0m cell_analysis \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 665\u001b[0m z_test \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlen\u001b[39m(img\u001b[38;5;241m.\u001b[39mshape) \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m2\u001b[39m\n\u001b[0;32m--> 666\u001b[0m \u001b[43m_analysis_loop\u001b[49m\u001b[43m(\u001b[49m\u001b[43mimg\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mk1\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mk2\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mimg_cell\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mthres\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlarge_thres\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mrdl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mz_test\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 667\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m disp \u001b[38;5;241m==\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[1;32m 668\u001b[0m \u001b[38;5;28mprint\u001b[39m(\n\u001b[1;32m 669\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAnalysed image file \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m Time elapsed: \u001b[39m\u001b[38;5;132;01m{:.3f}\u001b[39;00m\u001b[38;5;124m s\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m 670\u001b[0m i \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m, \u001b[38;5;28mlen\u001b[39m(files), time\u001b[38;5;241m.\u001b[39mtime() \u001b[38;5;241m-\u001b[39m start\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 673\u001b[0m flush\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 674\u001b[0m )\n",
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"File \u001b[0;32m~/Documents/Dropbox/Cambridge University Dropbox/Joseph Beckwith/Chemistry/Lee/Code/Python/pyRASP/src/RASPRoutines.py:567\u001b[0m, in \u001b[0;36mRASP_Routines.analyse_images.<locals>._analysis_loop\u001b[0;34m(img, k1, k2, img_cell, thres, large_thres, rdl, z_test)\u001b[0m\n\u001b[1;32m 542\u001b[0m img_cell \u001b[38;5;241m=\u001b[39m img_cell[:, :, z_planes[\u001b[38;5;241m0\u001b[39m] : z_planes[\u001b[38;5;241m1\u001b[39m]]\n\u001b[1;32m 543\u001b[0m (\n\u001b[1;32m 544\u001b[0m to_save,\n\u001b[1;32m 545\u001b[0m to_save_largeobjects,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 565\u001b[0m d\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39md,\n\u001b[1;32m 566\u001b[0m )\n\u001b[0;32m--> 567\u001b[0m \u001b[43mIO\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msave_analysis\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 568\u001b[0m \u001b[43m \u001b[49m\u001b[43mto_save\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 569\u001b[0m \u001b[43m \u001b[49m\u001b[43mto_save_largeobjects\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 570\u001b[0m \u001b[43m \u001b[49m\u001b[43manalysis_directory\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 571\u001b[0m \u001b[43m \u001b[49m\u001b[43mimtype\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 572\u001b[0m \u001b[43m \u001b[49m\u001b[43mprotein_string\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 573\u001b[0m \u001b[43m \u001b[49m\u001b[43mcell_string\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 574\u001b[0m \u001b[43m \u001b[49m\u001b[43mfiles\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 575\u001b[0m \u001b[43m \u001b[49m\u001b[43mi\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 576\u001b[0m \u001b[43m \u001b[49m\u001b[43mz_planes\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 577\u001b[0m \u001b[43m \u001b[49m\u001b[43mlo_mask\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 578\u001b[0m \u001b[43m \u001b[49m\u001b[43mcell_mask\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcell_mask\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mcell_analysis\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 579\u001b[0m \u001b[43m \u001b[49m\u001b[43mone_savefile\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mone_savefile\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 580\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m~/Documents/Dropbox/Cambridge University Dropbox/Joseph Beckwith/Chemistry/Lee/Code/Python/pyRASP/src/IOFunctions.py:105\u001b[0m, in \u001b[0;36mIO_Functions.save_analysis\u001b[0;34m(self, to_save, to_save_largeobjects, analysis_directory, imtype, protein_string, cell_string, files, i, z_planes, lo_mask, cell_mask, one_savefile)\u001b[0m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m to_save \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 100\u001b[0m to_save \u001b[38;5;241m=\u001b[39m to_save\u001b[38;5;241m.\u001b[39mwith_columns(\n\u001b[1;32m 101\u001b[0m image_filename\u001b[38;5;241m=\u001b[39mnp\u001b[38;5;241m.\u001b[39mfull_like(\n\u001b[1;32m 102\u001b[0m to_save[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_numpy(), files[i], dtype\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mobject\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 103\u001b[0m )\n\u001b[1;32m 104\u001b[0m )\n\u001b[0;32m--> 105\u001b[0m n_spots \u001b[38;5;241m=\u001b[39m \u001b[43mA_F\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcount_spots\u001b[49m\u001b[43m(\u001b[49m\u001b[43mto_save\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43marange\u001b[49m\u001b[43m(\u001b[49m\u001b[43mz_planes\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mz_planes\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 106\u001b[0m n_spots \u001b[38;5;241m=\u001b[39m n_spots\u001b[38;5;241m.\u001b[39mwith_columns(\n\u001b[1;32m 107\u001b[0m image_filename\u001b[38;5;241m=\u001b[39mnp\u001b[38;5;241m.\u001b[39mfull_like(\n\u001b[1;32m 108\u001b[0m n_spots[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mto_numpy(), files[i], dtype\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mobject\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 109\u001b[0m )\n\u001b[1;32m 110\u001b[0m )\n\u001b[1;32m 111\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
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"File \u001b[0;32m~/Documents/Dropbox/Cambridge University Dropbox/Joseph Beckwith/Chemistry/Lee/Code/Python/pyRASP/src/AnalysisFunctions.py:48\u001b[0m, in \u001b[0;36mAnalysis_Functions.count_spots\u001b[0;34m(self, database, z_planes, threshold)\u001b[0m\n\u001b[1;32m 36\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 37\u001b[0m \u001b[38;5;124;03mCounts spots per z plane, optionally with a threshold.\u001b[39;00m\n\u001b[1;32m 38\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 45\u001b[0m \u001b[38;5;124;03m polars.DataFrame: DataFrame with number of spots per z-plane.\u001b[39;00m\n\u001b[1;32m 46\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m threshold \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m---> 48\u001b[0m spots_per_plane \u001b[38;5;241m=\u001b[39m [np\u001b[38;5;241m.\u001b[39msum(database[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m==\u001b[39m z \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m) \u001b[38;5;28;01mfor\u001b[39;00m z \u001b[38;5;129;01min\u001b[39;00m z_planes]\n\u001b[1;32m 49\u001b[0m data \u001b[38;5;241m=\u001b[39m {\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m\"\u001b[39m: z_planes \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mn_spots\u001b[39m\u001b[38;5;124m\"\u001b[39m: spots_per_plane}\n\u001b[1;32m 50\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
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"File \u001b[0;32m~/Documents/Dropbox/Cambridge University Dropbox/Joseph Beckwith/Chemistry/Lee/Code/Python/pyRASP/src/AnalysisFunctions.py:48\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 36\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 37\u001b[0m \u001b[38;5;124;03mCounts spots per z plane, optionally with a threshold.\u001b[39;00m\n\u001b[1;32m 38\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 45\u001b[0m \u001b[38;5;124;03m polars.DataFrame: DataFrame with number of spots per z-plane.\u001b[39;00m\n\u001b[1;32m 46\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m threshold \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m---> 48\u001b[0m spots_per_plane \u001b[38;5;241m=\u001b[39m [\u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msum\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdatabase\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mz\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m==\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mz\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m z \u001b[38;5;129;01min\u001b[39;00m z_planes]\n\u001b[1;32m 49\u001b[0m data \u001b[38;5;241m=\u001b[39m {\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m\"\u001b[39m: z_planes \u001b[38;5;241m+\u001b[39m \u001b[38;5;241m1\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mn_spots\u001b[39m\u001b[38;5;124m\"\u001b[39m: spots_per_plane}\n\u001b[1;32m 50\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
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"File \u001b[0;32m~/.virtualenvs/pyRASP/lib/python3.10/site-packages/numpy/core/fromnumeric.py:2313\u001b[0m, in \u001b[0;36msum\u001b[0;34m(a, axis, dtype, out, keepdims, initial, where)\u001b[0m\n\u001b[1;32m 2310\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m out\n\u001b[1;32m 2311\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m res\n\u001b[0;32m-> 2313\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_wrapreduction\u001b[49m\u001b[43m(\u001b[49m\u001b[43ma\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msum\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkeepdims\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkeepdims\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 2314\u001b[0m \u001b[43m \u001b[49m\u001b[43minitial\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43minitial\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mwhere\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mwhere\u001b[49m\u001b[43m)\u001b[49m\n",
36-
"File \u001b[0;32m~/.virtualenvs/pyRASP/lib/python3.10/site-packages/numpy/core/fromnumeric.py:86\u001b[0m, in \u001b[0;36m_wrapreduction\u001b[0;34m(obj, ufunc, method, axis, dtype, out, **kwargs)\u001b[0m\n\u001b[1;32m 84\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m reduction(axis\u001b[38;5;241m=\u001b[39maxis, dtype\u001b[38;5;241m=\u001b[39mdtype, out\u001b[38;5;241m=\u001b[39mout, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mpasskwargs)\n\u001b[1;32m 85\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m---> 86\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mreduction\u001b[49m\u001b[43m(\u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpasskwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 88\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ufunc\u001b[38;5;241m.\u001b[39mreduce(obj, axis, dtype, out, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mpasskwargs)\n",
37-
"\u001b[0;31mTypeError\u001b[0m: Series.sum() got an unexpected keyword argument 'axis'"
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