diff --git a/.gitignore b/.gitignore index 067cc225711640e2804d23bc8b2ab3544778c998..7b2f7651ee0637317f69d3ff1aa415f25e3cf063 100644 --- a/.gitignore +++ b/.gitignore @@ -6,4 +6,6 @@ built-in-python/* extract_preprocessed_results/* neuropil_mapping/* -suite2p/* \ No newline at end of file +suite2p/* +interacting/* +pre-processing/* \ No newline at end of file diff --git a/alyx/0-Install_alyx_connexion(first time only).ipynb b/alyx/0-Install_alyx_connexion(first time only).ipynb index f9d446c782ba53244f965bb0bea4603dcb706abf..5083aaec5ace96a2dc8b61977007a2f44a90acf3 100644 --- a/alyx/0-Install_alyx_connexion(first time only).ipynb +++ b/alyx/0-Install_alyx_connexion(first time only).ipynb @@ -35,6 +35,41 @@ "- Finally, keep the database cache location to default. (used for database queries cache, not raw data temp folder. Very low data usage so there is no use to move this one in a specific location.)" ] }, + { + "cell_type": "markdown", + "id": "3c25ff9b-de52-4cf8-88c9-c848ad822ad4", + "metadata": {}, + "source": [ + "# Creating the connector object, cnx" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "27293ffb-8498-4eda-a4c9-c2f7a47ccf96", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "One (online, http://157.99.138.172:8080)\n" + ] + } + ], + "source": [ + "cnx = one.ONE() #et voilà !\n", + "print(cnx)" + ] + }, + { + "cell_type": "markdown", + "id": "38ecbc7e-be41-48f5-b368-f6dc0ac79c06", + "metadata": {}, + "source": [ + "# In case you need to redo a setup explicitely :" + ] + }, { "cell_type": "code", "execution_count": 8, @@ -75,33 +110,6 @@ "one.params.setup()" ] }, - { - "cell_type": "markdown", - "id": "3c25ff9b-de52-4cf8-88c9-c848ad822ad4", - "metadata": {}, - "source": [ - "# Creating the connector object, cnx" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "27293ffb-8498-4eda-a4c9-c2f7a47ccf96", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "One (online, http://157.99.138.172:8080)\n" - ] - } - ], - "source": [ - "cnx = one.ONE() #et voilà !\n", - "print(cnx)" - ] - }, { "cell_type": "markdown", "id": "92a5b383-85e7-46e2-9842-84991415226d", diff --git a/alyx/2-Renaming_to_ALF.ipynb b/alyx/2-Renaming_to_ALF.ipynb index 145fb13c4fac37616394388fcfad83a068787d45..9fedda773dff2c55913fe6aefe29470f60b19fc8 100644 --- a/alyx/2-Renaming_to_ALF.ipynb +++ b/alyx/2-Renaming_to_ALF.ipynb @@ -11,7 +11,8 @@ "import one, one.api\n", "import os\n", "import pandas as pd, numpy as np\n", - "import shutil" + "import shutil\n", + "Inflow.logging.enable_logging()" ] }, { @@ -21,7 +22,7 @@ "metadata": {}, "outputs": [], "source": [ - "cnx = one.api.ONE(base_url='http://157.99.138.172:8080')" + "cnx = one.ONE()" ] }, { @@ -33,17 +34,32 @@ }, "outputs": [], "source": [ - "selected_folder = r\"\\\\Mountcastle\\lab\\data\\ONE\\Adaptation\\wm25\\2022-08-05\\003\"" + "selected_folder = r\"\\\\cajal\\cajal_data2\\ONE\\Adaptation\\wm29\\2023-05-11\\001\"" + ] + }, + { + "cell_type": "markdown", + "id": "4b78436a-b75d-49b1-9e69-a6987a878a81", + "metadata": {}, + "source": [ + "## FINDS FILES AND RENAME THEM ACCORDING TO RULES SET IN HAISS LAB (to know what files contain wich type of information)\n", + "If you want to know the rules set in haiss lab, please visit : https://mountcastle/dokuwiki/doku.php?id=start#files_registration_rules" ] }, { "cell_type": "code", "execution_count": 4, - "id": "539cfe37-4ffa-4ad1-b9fc-480ac85e5019", - "metadata": { - "tags": [] - }, + "id": "d387a3a6-911f-4a57-9a66-3059fab21339", + "metadata": {}, "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[33;20mWARNING : apply_name_change : The apply_name_change function was called with option dry_run = True. It will only show you what files it would have renamed, without actually renaming them. If things look ok, you can set it to False to actually do the process. (one_alf.py:35) - 2023-05-17 16:58:49,611\u001b[0m\n", + "\u001b[33;20mWARNING : auto_rename_session_files_to_alf : All files supplied are already correctly renamed according to format rules. Passing (one_alf.py:26) - 2023-05-17 16:58:49,628\u001b[0m\n" + ] + }, { "data": { "text/html": [ @@ -72,595 +88,636 @@ " <tbody>\n", " <tr>\n", " <th>0</th>\n", - " <td>\\\\Mountcastle\\lab\\data\\ONE\\Adaptation\\wm25\\2022-08-05\\003\\figures\\fig.neuropil_mask.C1.png</td>\n", + " <td>\\\\cajal\\cajal_data2\\ONE\\Adaptation\\wm29\\2023-05-11\\001\\imaging_data\\imaging.fieldOfView.01.png</td>\n", " <td></td>\n", " </tr>\n", " <tr>\n", " <th>1</th>\n", - " <td>\\\\Mountcastle\\lab\\data\\ONE\\Adaptation\\wm25\\2022-08-05\\003\\figures\\fig.neuropil_mask.C1.svg</td>\n", + " <td>\\\\cajal\\cajal_data2\\ONE\\Adaptation\\wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00001.tif</td>\n", " <td></td>\n", " </tr>\n", " <tr>\n", " <th>2</th>\n", - " <td>\\\\Mountcastle\\lab\\data\\ONE\\Adaptation\\wm25\\2022-08-05\\003\\figures\\fig.neuropil_mask.D1.png</td>\n", + " <td>\\\\cajal\\cajal_data2\\ONE\\Adaptation\\wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00002.tif</td>\n", " 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'\\\\\\\\cajal\\\\cajal_data2\\\\ONE\\\\Adaptation\\\\wm29\\\\2023-05-11\\\\001\\\\imaging_data\\\\imaging.frames.00084.tif',\n", + " '\\\\\\\\cajal\\\\cajal_data2\\\\ONE\\\\Adaptation\\\\wm29\\\\2023-05-11\\\\001\\\\imaging_data\\\\imaging.frames.00085.tif',\n", + " '\\\\\\\\cajal\\\\cajal_data2\\\\ONE\\\\Adaptation\\\\wm29\\\\2023-05-11\\\\001\\\\trials.eventTimeline.tdms']" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "origin_pathes = Inflow.path.find.files(selected_folder, relative = False, levels = -1, get= \"files\" )#, re_pattern = '(?:.*\\.tif.*)|(?:.*\\.tdms)')\n", - "new_pathes = Inflow.path.one_alf.path_to_alf(origin_pathes,force = True)\n", - "with pd.option_context('display.max_rows', 500, 'display.max_columns', 500, 'display.width', 1000, \"expand_frame_repr\" , False,'max_colwidth', -1):\n", - " display(pd.DataFrame(np.array([origin_pathes, new_pathes]).T,columns=[\"origin_pathes\", \"new_pathes\"]))" - ] - }, - { - "cell_type": "code", - "execution_count": 160, - "id": "b87a2317-6bf9-43c2-bcdb-ef2e7b3af40a", - "metadata": {}, - "outputs": [], - "source": [ - "Inflow.path.one_alf.apply_name_change(origin_pathes, new_pathes)" + "Inflow.path.one_alf.auto_rename_session_files_to_alf(selected_folder)" ] } ], diff --git a/alyx/3-Populating_ALFs.ipynb b/alyx/3-Populating_ALFs.ipynb deleted file mode 100644 index b4b1e9ce599b1708fd4a653eaa3213d3230df989..0000000000000000000000000000000000000000 --- a/alyx/3-Populating_ALFs.ipynb +++ /dev/null @@ -1,497 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "fac48a6d-3fe1-4c11-ba6c-6c1be31065c4", - "metadata": {}, - "outputs": [], - "source": [ - "import Inflow\n", - "import one, one.api\n", - "import os\n", - "import pandas as pd, numpy as np\n", - "import shutil" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "9a3fc765-da04-4e20-bc95-c4a22c72ca80", - "metadata": {}, - "outputs": [], - "source": [ - "def make_homogeneous_empty_dataset_from_filelist(files,session_details,repository_name):\n", - " import one\n", - " #Verify all goes well for a batch of alf file\n", - " cnx = one.api.ONE()\n", - " repo_path = cnx.get_data_repository_path(repository_name)\n", - " \n", - " common_alf_type = {}\n", - " for file in files:\n", - " alf_name = os.path.relpath(file, start = os.path.relpath(session_details[\"fullpath\"], start = repo_path)) \n", - " if len(common_alf_type):\n", - " alf_type = one.alf.files.rel_path_parts( alf_name.replace(\"\\\\\",\"/\"), as_dict = True )\n", - " if alf_type[\"collection\"] != common_alf_type[\"collection\"] :\n", - " raise ValueError(\"Registering several files under a same dataset require them being under the same collection (session subdirectory)\")\n", - " if alf_type[\"revision\"] != common_alf_type[\"revision\"]:\n", - " raise NotImlementedError\n", - " if alf_type[\"object\"] != common_alf_type[\"object\"]:\n", - " raise ValueError(\"Registering several files under a same dataset require them having the same object name (first name before dot)\")\n", - " if alf_type[\"attribute\"] != common_alf_type[\"attribute\"]:\n", - " raise ValueError(\"Registering several files under a same dataset require them having the same attribute name (second name before dot)\")\n", - " if alf_type[\"extension\"] != common_alf_type[\"extension\"]:\n", - " raise ValueError(\"Registering several files under a same dataset require them having the same extension (second name before dot)\")\n", - " else :\n", - " common_alf_type = one.alf.files.rel_path_parts( alf_name.replace(\"\\\\\",\"/\"), as_dict = True )\n", - " \n", - " d = {\"name\" : common_alf_type[\"object\"]+\".\"+common_alf_type[\"attribute\"]+\".\"+common_alf_type[\"extension\"],\n", - " 'created_by': one.params.get().ALYX_LOGIN,\n", - " \"dataset_type\" : common_alf_type[\"object\"]+\".\"+common_alf_type[\"attribute\"],\n", - " \"data_format\" : common_alf_type[\"extension\"],\n", - " \"collection\" : common_alf_type[\"collection\"],\n", - " \"session\" : session_details[\"url\"],\n", - " }\n", - " \n", - " new_dataset = cnx.alyx.rest(\"datasets\",\"create\",data = d )\n", - " \n", - " return new_dataset\n", - "\n", - "def add_files_to_empty_homogeneous_dataset(files, dataset_dict, repository_name ):\n", - " #a programmatic version :\n", - " #repo = cnx.alyx.rest(\"data-repository\",\"read\",repository_name)\n", - " for file in files :\n", - " d = {\"dataset\" : dataset_dict[\"url\"],\n", - " \"data_repository\" : repository_name,\n", - " \"relative_path\" : file,\n", - " \"exists\" : True\n", - " }\n", - " new_file_record = cnx.alyx.rest(\"files\",\"create\",data = d )" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "b1b98675-aa43-4c85-add0-e4fed6700b6a", - "metadata": {}, - "outputs": [], - "source": [ - "selected_folder = r\"\\\\Mountcastle\\lab\\data\\ONE\\Adaptation\\wm25\\2022-08-05\\003\"\n", - "origin_pathes = Inflow.path.find.files(selected_folder, relative = False, levels = -1, get= \"files\" )#, re_pattern = '(?:.*\\.tif.*)|(?:.*\\.tdms)')" - ] - }, - { - "cell_type": "markdown", - "id": "3248de09-b21c-4d19-8af0-d0c9105c1530", - "metadata": {}, - "source": [ - "## FINDS INDIVIDUAL HOMOGENEOUS DATASETS AND ADD THEM (care : doesn't check for already existing identical datasets)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "06215e73-2e16-4d80-9ff0-9823176a653c", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "<div>\n", - "<style scoped>\n", - " .dataframe tbody tr th:only-of-type {\n", - " vertical-align: middle;\n", - " }\n", - "\n", - " .dataframe tbody tr th {\n", - " vertical-align: top;\n", - " }\n", - "\n", - " .dataframe thead th {\n", - " text-align: right;\n", - " }\n", - "</style>\n", - "<table border=\"1\" class=\"dataframe\">\n", - " <thead>\n", - " <tr style=\"text-align: right;\">\n", - " <th></th>\n", - " <th>root</th>\n", - " 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"text": [ - "['\\\\\\\\Mountcastle\\\\lab\\\\data\\\\ONE\\\\Adaptation\\\\wm25\\\\2022-08-05\\\\003\\\\trials.eventTimeline.tdms']\n", - "\\\\Mountcastle\\lab\\data\\ONE\\Adaptation\n", - "['wm25\\\\2022-08-05\\\\003\\\\trials.eventTimeline.tdms']\n" - ] - } - ], - "source": [ - "results = [one.alf.files.absolute_session_path_parts(file, as_dict = True, assert_valid = False) for file in origin_pathes]\n", - "fileparts_df = pd.DataFrame(results)\n", - "for collection_name, collection_selection in fileparts_df.groupby(\"collection\",dropna=False):\n", - " for filenames, files_collections in collection_selection.groupby([\"object\",\"attribute\"],dropna=False):\n", - " if files_collections.isna().all().all() : continue # if file is realy not supporting the ALF standard, we won't be able to recompose it with one.alf.spec.to_full_path, so we won't include it in addible datasets anyway\n", - " if files_collections.iloc[0][\"collection\"] == \"preprocessing_saves\" : continue\n", - " if files_collections.iloc[0][\"collection\"] == \"figures\" : continue\n", - " \n", - " #print(filenames)\n", - " display(files_collections)\n", - " files = files_collections.apply(lambda row : one.alf.spec.to_full_path(**row) ,axis = 1).tolist()\n", - " print(files)\n", - " bools = [os.path.isfile(file) for file in files]\n", - " root_path = files_collections.iloc[0][\"root\"]\n", - " print(root_path)\n", - " if sum(bools) == len(bools) : # all files have been reconstitued correctly and correspond to existing files\n", - " files = [os.path.relpath(file, start = root_path) for file in files]\n", - " print(files)\n", - "\n", - " #new_dataset = make_homogeneous_empty_dataset_from_filelist(files,session_details,repository_name)\n", - " #add_files_to_empty_homogeneous_dataset(files,new_dataset,repository_name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.8.13" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/alyx/3-Registering_ALFs_files.ipynb b/alyx/3-Registering_ALFs_files.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..156411daa79bc5c39f356b39d60b0a5a8eed7808 --- /dev/null +++ b/alyx/3-Registering_ALFs_files.ipynb @@ -0,0 +1,521 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 3, + "id": "fac48a6d-3fe1-4c11-ba6c-6c1be31065c4", + "metadata": {}, + "outputs": [], + "source": [ + "import Inflow\n", + "import one, one.api\n", + "import os\n", + "import pandas as pd, numpy as np\n", + "import shutil\n", + "Inflow.logging.enable_logging()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "f77dc67b-9f9b-44d3-91c3-1698fcafb490", + "metadata": {}, + "outputs": [], + "source": [ + "cnx = one.ONE()\n", + "cnx.set_data_access_mode(\"remote\")\n", + "#cnx.alyx.delete_cache()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "b1b98675-aa43-4c85-add0-e4fed6700b6a", + "metadata": {}, + "outputs": [], + "source": [ + "selected_folder = r\"\\\\cajal\\cajal_data2\\ONE\\Adaptation\\wm29\\2023-05-11\\001\\imaging_data\"\n", + "repository_name = \"Cajal2Adaptation\"\n", + "\n", + "origin_pathes = Inflow.path.find.files(selected_folder, relative = False, levels = -1, get = \"files\" )#, re_pattern = '(?:.*\\.tif.*)|(?:.*\\.tdms)')" + ] + }, + { + "cell_type": "markdown", + "id": "3248de09-b21c-4d19-8af0-d0c9105c1530", + "metadata": {}, + "source": [ + "## FINDS INDIVIDUAL HOMOGENEOUS DATASETS AND REGISTER THEM TO THE SESSION IN THE DATABASEFINDS INDIVIDUAL HOMOGENEOUS DATASETS AND REGISTER THEM TO THE SESSION IN THE DATABASE" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "318c1f31-b8ca-4cdf-9830-96bae122b2b5", + 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Using it to attach files instead of creating a new one. (one_alf.py:172) - 2023-05-17 16:41:55,753\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.fieldOfView.01.png already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:55,854\u001b[0m\n" + ] + }, + { + "data": { + "text/html": [ + "<div>\n", + "<style scoped>\n", + " .dataframe tbody tr th:only-of-type {\n", + " vertical-align: middle;\n", + " }\n", + "\n", + " .dataframe tbody tr th {\n", + " vertical-align: top;\n", + " }\n", + "\n", + " .dataframe thead th {\n", + " text-align: right;\n", + " }\n", + "</style>\n", + "<table border=\"1\" class=\"dataframe\">\n", + " <thead>\n", + " <tr style=\"text-align: right;\">\n", + " <th></th>\n", + " <th>root</th>\n", + " <th>lab</th>\n", + " <th>subject</th>\n", + " <th>date</th>\n", + " <th>number</th>\n", + " <th>collection</th>\n", + " <th>revision</th>\n", + " <th>namespace</th>\n", + " <th>object</th>\n", + " <th>attribute</th>\n", + " 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Using it to attach files instead of creating a new one. (one_alf.py:172) - 2023-05-17 16:41:56,048\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00001.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,104\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00002.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,105\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00003.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,105\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00004.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,106\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00005.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,107\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00006.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,107\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00007.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,108\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00008.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,109\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00009.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,109\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00010.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,110\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00011.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,111\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00012.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,111\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00013.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,112\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00014.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,112\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00015.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,113\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00016.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,114\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00017.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,114\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00018.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,115\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00019.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,115\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00020.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,116\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00021.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,117\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00022.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,117\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00023.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,117\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00024.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,118\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00025.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,119\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00026.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,119\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00027.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,120\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00028.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,120\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00029.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,121\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00030.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,121\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00031.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,122\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00032.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,123\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00033.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,123\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00034.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,124\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00035.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,124\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00036.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,125\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00037.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,126\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00038.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,126\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00039.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,127\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00040.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,128\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00041.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,128\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00042.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,129\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00043.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,129\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00044.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,130\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00045.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,131\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00046.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,131\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00047.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,132\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00048.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,133\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00049.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,133\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00050.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,134\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00051.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,134\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00052.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,135\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00053.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,135\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00054.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,136\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00055.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,137\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00056.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,138\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00057.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,138\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00058.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,139\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00059.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,140\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00060.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,140\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00061.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,141\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00062.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,141\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00063.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,142\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00064.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,143\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00065.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,143\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00066.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,144\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00067.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,145\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00068.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,145\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00069.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,146\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00070.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,147\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00071.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,147\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00072.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,148\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00073.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,149\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00074.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,149\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00075.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,150\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00076.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,150\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00077.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,151\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00078.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,152\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00079.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,152\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00080.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,153\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00081.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,154\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00082.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,154\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00083.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,154\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00084.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,155\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00085.tif already exist in dataset, it was not added (one_alf.py:204) - 2023-05-17 16:41:56,156\u001b[0m\n" + ] + } + ], + "source": [ + "Inflow.path.one_alf.register_files(origin_pathes,selected_folder,repository_name, dry_run = False)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/alyx/3.5-Rename_+_Register.ipynb b/alyx/3.5-Rename_+_Register.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..2c5409f4cd99c346984a50805dbb3877f561dcf2 --- /dev/null +++ b/alyx/3.5-Rename_+_Register.ipynb @@ -0,0 +1,802 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 6, + "id": "d91fa970-c26d-4c95-a8d9-c364b68348d3", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[38;20mDEBUG : enable_logging : Setting logger level to 10 (logging.py:78) - 2023-05-17 20:45:51,317\u001b[0m\n", + "\u001b[38;20mDEBUG : enable_logging : Logger is already configured, skipping instanciation (logging.py:79) - 2023-05-17 20:45:51,318\u001b[0m\n", + "\u001b[38;20mDEBUG : enable_logging : setting <TimedRotatingFileHandler C:\\Users\\tjostmou\\Downloads\\.python_logs\\pylogs.log (DEBUG)> handler level to 10 (logging.py:82) - 2023-05-17 20:45:51,318\u001b[0m\n", + "\u001b[38;20mDEBUG : enable_logging : setting <StreamHandler stdout (DEBUG)> handler level to 10 (logging.py:82) - 2023-05-17 20:45:51,319\u001b[0m\n" + ] + } + ], + "source": [ + "import Inflow\n", + "import one, one.api\n", + "import os\n", + "import pandas as pd, numpy as np\n", + "import shutil\n", + "Inflow.logging.enable_logging(level = \"DEBUG\")" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "d66a0717-991a-468f-bc62-53311355349f", + "metadata": {}, + "outputs": [], + "source": [ + "cnx = one.ONE()\n", + "cnx.alyx.delete_cache()" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "01f51282-dff6-4fb8-a2c7-bf6d089f1d67", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "selected_session_folder = r\"\\\\cajal\\cajal_data2\\ONE\\Adaptation\\wm29\\2023-05-11\\001\"\n", + "dry_run = False" + ] + }, + { + "cell_type": "markdown", + "id": "a8ca8efc-2a8b-4479-86d2-1d12dd8ae89f", + "metadata": { + "tags": [] + }, + "source": [ + "## RENAME FILES AND REGISTER THEM\n", + " - First : FINDS FILES AND RENAME THEM ACCORDING TO RULES SET IN HAISS LAB (to know what files contain wich type of information)\n", + " If you want to know the rules set in haiss lab, please visit : https://mountcastle/dokuwiki/doku.php?id=start#files_registration_rules\n", + " - Second : FINDS INDIVIDUAL HOMOGENEOUS DATASETS AND REGISTER THEM TO THE SESSION IN THE DATABASE" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "70ced300-bff7-4218-bb21-ad576baca746", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[94;20mINFO : auto_rename_session_files_to_alf : All files supplied are already correctly renamed according to format rules. Passing\u001b[0m\n", + "\u001b[94;20mINFO : register_files : Found a common data-repository in the filepaths to use for registering : Cajal2Adaptation\u001b[0m\n" + ] + }, + { + "data": { + "text/html": [ + "<div>\n", + "<style scoped>\n", + " .dataframe tbody tr th:only-of-type {\n", + " vertical-align: middle;\n", + " }\n", + "\n", + " .dataframe tbody tr th {\n", + " vertical-align: top;\n", + " }\n", + "\n", + " .dataframe thead th {\n", + " text-align: right;\n", + " }\n", + "</style>\n", + "<table border=\"1\" class=\"dataframe\">\n", + " <thead>\n", + " <tr style=\"text-align: right;\">\n", + " <th></th>\n", + " <th>root</th>\n", + " <th>lab</th>\n", + " <th>subject</th>\n", + " <th>date</th>\n", + " <th>number</th>\n", + " <th>collection</th>\n", + " <th>revision</th>\n", + " <th>namespace</th>\n", + " <th>object</th>\n", + " <th>attribute</th>\n", + " <th>timescale</th>\n", + " <th>extra</th>\n", + " <th>extension</th>\n", + " </tr>\n", + " </thead>\n", + " <tbody>\n", + " <tr>\n", + " <th>0</th>\n", + " <td>//cajal/cajal_data2/ONE/Adaptation</td>\n", + " <td>None</td>\n", + " <td>wm29</td>\n", + " <td>2023-05-11</td>\n", + " <td>001</td>\n", + " <td>imaging_data</td>\n", + " <td>None</td>\n", + " <td>None</td>\n", + " <td>imaging</td>\n", + " <td>fieldOfView</td>\n", + " <td>None</td>\n", + " <td>01</td>\n", + " <td>png</td>\n", + " </tr>\n", + " </tbody>\n", + "</table>\n", + "</div>" + ], + "text/plain": [ + " root lab subject date number \\\n", + "0 //cajal/cajal_data2/ONE/Adaptation None wm29 2023-05-11 001 \n", + "\n", + " collection revision namespace object attribute timescale extra \\\n", + "0 imaging_data None None imaging fieldOfView None 01 \n", + "\n", + " extension \n", + "0 png " + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.fieldOfView.01.png (one_alf.py:170) - 2023-05-17 20:45:54,691\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : checking existing dataset : {'id': '01300074-de8b-4c1a-8450-658260625364', 'name': 'imaging.fieldOfView.png', 'dataset_type': 'imaging.fieldOfView', 'data_url': None, 'url': 'http://157.99.138.172/datasets/01300074-de8b-4c1a-8450-658260625364', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:213) - 2023-05-17 20:45:54,693\u001b[0m\n", + "\u001b[94;20mINFO : make_homogeneous_empty_dataset_from_filelist : The dataset imaging.fieldOfView.png was already existing. Using it to attach files instead of creating a new one.\u001b[0m\n", + "\u001b[38;20mDEBUG : add_files_to_empty_homogeneous_dataset : dataset_dict : {'id': '01300074-de8b-4c1a-8450-658260625364', 'name': 'imaging.fieldOfView.png', 'dataset_type': 'imaging.fieldOfView', 'data_url': None, 'url': 'http://157.99.138.172/datasets/01300074-de8b-4c1a-8450-658260625364', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:238) - 2023-05-17 20:45:54,711\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.fieldOfView.01.png already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:54,801\u001b[0m\n" + ] + }, + { + "data": { + "text/html": [ + "<div>\n", + "<style scoped>\n", + " .dataframe tbody tr th:only-of-type {\n", + " vertical-align: middle;\n", + " }\n", + "\n", + " .dataframe tbody tr th {\n", + " 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make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00002.tif (one_alf.py:170) - 2023-05-17 20:45:54,993\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00002'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:54,993\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00003.tif (one_alf.py:170) - 2023-05-17 20:45:54,994\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00003'), 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('timescale', None), ('extra', '00050'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,061\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00051.tif (one_alf.py:170) - 2023-05-17 20:45:55,061\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00051'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,062\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00052.tif (one_alf.py:170) - 2023-05-17 20:45:55,062\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 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20:45:55,070\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00058.tif (one_alf.py:170) - 2023-05-17 20:45:55,070\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00058'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,071\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00059.tif (one_alf.py:170) - 2023-05-17 20:45:55,072\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), 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make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00063'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,078\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00064.tif (one_alf.py:170) - 2023-05-17 20:45:55,078\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00064'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,079\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : 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20:45:55,082\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00067.tif (one_alf.py:170) - 2023-05-17 20:45:55,082\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00067'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,083\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00068.tif (one_alf.py:170) - 2023-05-17 20:45:55,084\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), 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make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00072'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,090\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00073.tif (one_alf.py:170) - 2023-05-17 20:45:55,091\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00073'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,091\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00074.tif (one_alf.py:170) - 2023-05-17 20:45:55,092\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00074'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,093\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00075.tif (one_alf.py:170) - 2023-05-17 20:45:55,093\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00075'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,094\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00076.tif (one_alf.py:170) - 2023-05-17 20:45:55,095\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00076'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,095\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00077.tif (one_alf.py:170) - 2023-05-17 20:45:55,096\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00077'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,096\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00078.tif (one_alf.py:170) - 2023-05-17 20:45:55,097\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00078'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,098\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00079.tif (one_alf.py:170) - 2023-05-17 20:45:55,099\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00079'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,099\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00080.tif (one_alf.py:170) - 2023-05-17 20:45:55,100\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00080'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,101\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00081.tif (one_alf.py:170) - 2023-05-17 20:45:55,101\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00081'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,102\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00082.tif (one_alf.py:170) - 2023-05-17 20:45:55,103\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00082'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,103\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00083.tif (one_alf.py:170) - 2023-05-17 20:45:55,104\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00083'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,105\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00084.tif (one_alf.py:170) - 2023-05-17 20:45:55,105\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00084'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,106\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\imaging_data\\imaging.frames.00085.tif (one_alf.py:170) - 2023-05-17 20:45:55,106\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file parts are : OrderedDict([('collection', 'imaging_data'), ('revision', None), ('namespace', None), ('object', 'imaging'), ('attribute', 'frames'), ('timescale', None), ('extra', '00085'), ('extension', 'tif')]) (one_alf.py:184) - 2023-05-17 20:45:55,107\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : checking existing dataset : {'id': '01300074-de8b-4c1a-8450-658260625364', 'name': 'imaging.fieldOfView.png', 'dataset_type': 'imaging.fieldOfView', 'data_url': None, 'url': 'http://157.99.138.172/datasets/01300074-de8b-4c1a-8450-658260625364', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:213) - 2023-05-17 20:45:55,109\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : checking existing dataset : {'id': '15675759-5f95-45bf-a348-d40202a69fea', 'name': 'imaging.frames.tif', 'dataset_type': 'imaging.frames', 'data_url': None, 'url': 'http://157.99.138.172/datasets/15675759-5f95-45bf-a348-d40202a69fea', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:213) - 2023-05-17 20:45:55,109\u001b[0m\n", + "\u001b[94;20mINFO : make_homogeneous_empty_dataset_from_filelist : The dataset imaging.frames.tif was already existing. Using it to attach files instead of creating a new one.\u001b[0m\n", + "\u001b[38;20mDEBUG : add_files_to_empty_homogeneous_dataset : dataset_dict : {'id': '15675759-5f95-45bf-a348-d40202a69fea', 'name': 'imaging.frames.tif', 'dataset_type': 'imaging.frames', 'data_url': None, 'url': 'http://157.99.138.172/datasets/15675759-5f95-45bf-a348-d40202a69fea', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:238) - 2023-05-17 20:45:55,124\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00001.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,165\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00002.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,165\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00003.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,166\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00004.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,167\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00005.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,167\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00006.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,168\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00007.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,169\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00008.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,169\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00009.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,170\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00010.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,170\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00011.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,171\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00012.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,172\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00013.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,172\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00014.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,173\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00015.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,173\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00016.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,174\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00017.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,175\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00018.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,175\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00019.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,176\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00020.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,177\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00021.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,177\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00022.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,178\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00023.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,178\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00024.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,179\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00025.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,180\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00026.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,180\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00027.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,181\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00028.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,181\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00029.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,182\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00030.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,182\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00031.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,183\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00032.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,183\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00033.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,184\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00034.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,184\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00035.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,185\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00036.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,186\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00037.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,186\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00038.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,187\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00039.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,187\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00040.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,188\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00041.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,189\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00042.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,190\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00043.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,190\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00044.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,191\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00045.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,191\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00046.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,192\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00047.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,193\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00048.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,193\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00049.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,194\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00050.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,194\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00051.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,195\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00052.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,195\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00053.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,196\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00054.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,197\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00055.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,197\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00056.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,198\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00057.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,198\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00058.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,199\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00059.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,199\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00060.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,200\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00061.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,201\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00062.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,201\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00063.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,202\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00064.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,202\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00065.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,203\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00066.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,204\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00067.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,204\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00068.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,205\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00069.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,206\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00070.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,206\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00071.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,207\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00072.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,207\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00073.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,208\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00074.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,209\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00075.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,209\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00076.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,210\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00077.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,211\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00078.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,211\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00079.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,212\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00080.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,212\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00081.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,213\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00082.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,213\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00083.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,214\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00084.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,215\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/imaging_data/imaging.frames.00085.tif already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,215\u001b[0m\n" + ] + }, + { + "data": { + "text/html": [ + "<div>\n", + "<style scoped>\n", + " .dataframe tbody tr th:only-of-type {\n", + " vertical-align: middle;\n", + " }\n", + "\n", + " .dataframe tbody tr th {\n", + " vertical-align: top;\n", + " }\n", + "\n", + " .dataframe thead th {\n", + " text-align: right;\n", + " }\n", + "</style>\n", + "<table border=\"1\" class=\"dataframe\">\n", + " <thead>\n", + " <tr style=\"text-align: right;\">\n", + " <th></th>\n", + " <th>root</th>\n", + " <th>lab</th>\n", + " <th>subject</th>\n", + " <th>date</th>\n", + " <th>number</th>\n", + " <th>collection</th>\n", + " <th>revision</th>\n", + " <th>namespace</th>\n", + " <th>object</th>\n", + " <th>attribute</th>\n", + " <th>timescale</th>\n", + " <th>extra</th>\n", + " <th>extension</th>\n", + " </tr>\n", + " </thead>\n", + " <tbody>\n", + " <tr>\n", + " <th>86</th>\n", + " <td>//cajal/cajal_data2/ONE/Adaptation</td>\n", + " <td>None</td>\n", + " <td>wm29</td>\n", + " <td>2023-05-11</td>\n", + " <td>001</td>\n", + " <td>None</td>\n", + " <td>None</td>\n", + " <td>None</td>\n", + " <td>trials</td>\n", + " <td>eventTimeline</td>\n", + " <td>None</td>\n", + " <td>None</td>\n", + " <td>tdms</td>\n", + " </tr>\n", + " </tbody>\n", + "</table>\n", + "</div>" + ], + "text/plain": [ + " root lab subject date number \\\n", + "86 //cajal/cajal_data2/ONE/Adaptation None wm29 2023-05-11 001 \n", + "\n", + " collection revision namespace object attribute timescale extra \\\n", + "86 None None None trials eventTimeline None None \n", + "\n", + " extension \n", + "86 tdms " + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : file path is : wm29\\2023-05-11\\001\\trials.eventTimeline.tdms (one_alf.py:170) - 2023-05-17 20:45:55,370\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : checking existing dataset : {'id': '01300074-de8b-4c1a-8450-658260625364', 'name': 'imaging.fieldOfView.png', 'dataset_type': 'imaging.fieldOfView', 'data_url': None, 'url': 'http://157.99.138.172/datasets/01300074-de8b-4c1a-8450-658260625364', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:213) - 2023-05-17 20:45:55,372\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : checking existing dataset : {'id': '15675759-5f95-45bf-a348-d40202a69fea', 'name': 'imaging.frames.tif', 'dataset_type': 'imaging.frames', 'data_url': None, 'url': 'http://157.99.138.172/datasets/15675759-5f95-45bf-a348-d40202a69fea', 'file_size': None, 'hash': None, 'version': None, 'collection': 'imaging_data', 'revision': None, 'default_revision': 'True'} (one_alf.py:213) - 2023-05-17 20:45:55,373\u001b[0m\n", + "\u001b[38;20mDEBUG : make_homogeneous_empty_dataset_from_filelist : checking existing dataset : {'id': '0b42206f-453c-4571-9bfa-b7fc0f3cb614', 'name': 'trials.eventTimeline.tdms', 'dataset_type': 'trials.eventTimeline', 'data_url': None, 'url': 'http://157.99.138.172/datasets/0b42206f-453c-4571-9bfa-b7fc0f3cb614', 'file_size': None, 'hash': None, 'version': None, 'collection': None, 'revision': None, 'default_revision': 'True'} (one_alf.py:213) - 2023-05-17 20:45:55,374\u001b[0m\n", + "\u001b[94;20mINFO : make_homogeneous_empty_dataset_from_filelist : The dataset trials.eventTimeline.tdms was already existing. Using it to attach files instead of creating a new one.\u001b[0m\n", + "\u001b[38;20mDEBUG : add_files_to_empty_homogeneous_dataset : dataset_dict : {'id': '0b42206f-453c-4571-9bfa-b7fc0f3cb614', 'name': 'trials.eventTimeline.tdms', 'dataset_type': 'trials.eventTimeline', 'data_url': None, 'url': 'http://157.99.138.172/datasets/0b42206f-453c-4571-9bfa-b7fc0f3cb614', 'file_size': None, 'hash': None, 'version': None, 'collection': None, 'revision': None, 'default_revision': 'True'} (one_alf.py:238) - 2023-05-17 20:45:55,389\u001b[0m\n", + "\u001b[31;20mERROR : add_files_to_empty_homogeneous_dataset : File wm29/2023-05-11/001/trials.eventTimeline.tdms already exist in dataset, it was not added (one_alf.py:253) - 2023-05-17 20:45:55,464\u001b[0m\n" + ] + } + ], + "source": [ + "files_list = Inflow.path.one_alf.auto_rename_session_files_to_alf(selected_session_folder, dry_run = dry_run)\n", + "Inflow.path.one_alf.register_files(files_list,selected_session_folder, dry_run = dry_run)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/my_first_analysis/multi-session_classifiers.ipynb b/my_first_analysis/multi-session_classifiers.ipynb index a15050789970c4733dbf8b2fcb5ae20352d6ecb5..97ff6be879871dba069a53c064af137e5567824d 100644 --- a/my_first_analysis/multi-session_classifiers.ipynb +++ b/my_first_analysis/multi-session_classifiers.ipynb @@ -41,35 +41,10 @@ "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "text/plain": [ - "<function ResearchProjects.adaptation.select.cells_labelled(rois_df, iscell=True, **kwargs)>" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/plain": [ - "\u001b[1;31mType:\u001b[0m module\n", - "\u001b[1;31mString form:\u001b[0m <module 'ResearchProjects.core' from 'c:\\\\users\\\\tjostmou\\\\documents\\\\python\\\\__packages__\\\\researchprojects\\\\ResearchProjects\\\\core.py'>\n", - "\u001b[1;31mFile:\u001b[0m c:\\users\\tjostmou\\documents\\python\\__packages__\\researchprojects\\researchprojects\\core.py\n", - "\u001b[1;31mDocstring:\u001b[0m <no docstring>\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "connector = one.ONE()\n", - "connector.set_data_access_mode('local')\n", - "ResearchProjects.core?\n", - "ResearchProjects.adaptation.select.cells_labelled\n", - "display(ResearchProjects.adaptation.select.cells_labelled)" + "connector.set_data_access_mode('local')" ] }, { @@ -373,9 +348,7 @@ "groups = adaptation.select.get_groups_by_index(trials_roi_df,\"trial#\")\n", "\n", "for indices, roi_group in groups: \n", - " #if not roi_group.iloc[0][\"in_any_barrel\"] :\n", - " # continue\n", - " #print(indices)\n", + "\n", " indices = {key : value for key, value in zip(groups.keys,indices)}\n", " print(f\"ROI {indices} of {len(roi_group)}\",end = \"\\r\")\n", " \n", @@ -387,9 +360,28 @@ " results = adaptation.classifiers.get_loocv_results(group_df,features_key = \"neuronal_features\", classes_key = \"target_amplitude\", n_estimators = 100, n_jobs = 30)\n", " conditions.update(results)\n", " conditions.update(indices)\n", - " rois_classifiers.append(conditions)\n" + " rois_classifiers.append(conditions)" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "9c1f17f2-7116-49fd-bcfc-27a20a83ce30", + "metadata": {}, + "outputs": [], + "source": [ + "time_keys = trials_roi_df.columns[0:5]\n", + "criterias = trials_roi_df.columns[5:]" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "1fc5710c-5905-4451-9875-c10455d4d677", + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": 13,