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Trialization #4

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merged 9 commits into from
Apr 30, 2022
Merged

Trialization #4

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a9e78a0
WIP trialization
CBroz1 Apr 27, 2022
c1e8196
WIP add ingest funcs
CBroz1 Apr 27, 2022
70c2e00
Merge branch 'main' of https://github.com/kabilar/workflow-miniscope …
CBroz1 Apr 28, 2022
b244abc
revised notebooks to reflect updated element
CBroz1 Apr 28, 2022
44d8072
WIP trialization nb 03, 05, 07. Errs on each
CBroz1 Apr 28, 2022
008f96c
Notebooks 05, 07 successful run
CBroz1 Apr 28, 2022
0f3383f
Update workflow_miniscope/analysis.py
kabilar Apr 29, 2022
8e066c1
Update workflow_miniscope/analysis.py
kabilar Apr 29, 2022
97d4d53
Update workflow_miniscope/analysis.py
kabilar Apr 29, 2022
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13 changes: 7 additions & 6 deletions notebooks/00-data-download-optional.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,8 @@
"metadata": {},
"outputs": [],
"source": [
"client.download('workflow-miniscope-test-set', target_directory='/tmp/example_data', revision='v1')"
"client.download('workflow-miniscope-test-set', \n",
" target_directory='/tmp/example_data', revision='v1')"
]
},
{
Expand Down Expand Up @@ -142,12 +143,12 @@
],
"metadata": {
"jupytext": {
"formats": "ipynb,scripts//py",
"main_language": "python"
"formats": "ipynb,scripts//py"
},
"kernelspec": {
"display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",
"name": "python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c"
"display_name": "venv-nwb",
"language": "python",
"name": "venv-nwb"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -159,7 +160,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.9"
"version": "3.8.11"
}
},
"nbformat": 4,
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3 changes: 2 additions & 1 deletion notebooks/01-configure.ipynb
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Expand Up @@ -197,7 +197,8 @@
],
"metadata": {
"jupytext": {
"formats": "ipynb,scripts//py"
"formats": "ipynb,scripts//py",
"main_language": "python"
},
"kernelspec": {
"display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",
Expand Down
102 changes: 55 additions & 47 deletions notebooks/02-workflow-structure-optional.ipynb
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Expand Up @@ -47,11 +47,14 @@
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ Each module contains a schema object that enables interaction with the schema in the database."
]
"cell_type": "code",
"execution_count": null,
"id": "693929a9",
"metadata": {
"title": "Each module contains a schema object that enables interaction with the schema in the database."
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
Expand All @@ -65,11 +68,14 @@
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ The table classes in the module corresponds to a table in the schema in the database."
]
"cell_type": "code",
"execution_count": null,
"id": "d0ee126a",
"metadata": {
"title": "The table classes in the module corresponds to a table in the schema in the database."
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
Expand All @@ -90,9 +96,9 @@
"title": "The first time importing the modules, empty schemas and tables will be created in the database."
},
"source": [
"+ By importing the modules for the first time, the schemas and tables will be created inside the database.\n",
"# + By importing the modules for the first time, the schemas and tables will be created inside the database.\n",
"\n",
"+ Once created, importing modules will not create schemas and tables again, but the existing schemas/tables can be accessed and manipulated by the modules."
"# + Once created, importing modules will not create schemas and tables again, but the existing schemas/tables can be accessed and manipulated by the modules."
]
},
{
Expand All @@ -104,7 +110,7 @@
"source": [
"## DataJoint tools to explore schemas and tables\n",
"\n",
"+ `dj.list_schemas()`: list all schemas a user has access to in the current database"
"# + `dj.list_schemas()`: list all schemas a user has access to in the current database"
]
},
{
Expand All @@ -119,11 +125,14 @@
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ `dj.Diagram()`: plot tables and dependencies in a schema. "
]
"cell_type": "code",
"execution_count": null,
"id": "687dbcb3",
"metadata": {
"title": "`dj.Diagram()`: plot tables and dependencies in a schema."
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
Expand Down Expand Up @@ -205,7 +214,7 @@
"title": "`heading`:"
},
"source": [
"+ `describe()`: show table definition with foreign key references."
"# + `describe()`: show table definition with foreign key references."
]
},
{
Expand All @@ -218,11 +227,14 @@
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ `heading`: show attribute definitions regardless of foreign key references"
]
"cell_type": "code",
"execution_count": null,
"id": "08837864",
"metadata": {
"title": "`heading`: show attribute definitions regardless of foreign key references"
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
Expand All @@ -243,7 +255,7 @@
"source": [
"# DataJoint Elements installed in `workflow-miniscope`\n",
"\n",
"+ [`lab`](https://github.com/datajoint/element-lab): lab management related information, such as Lab, User, Project, Protocol, Source."
"# + [`lab`](https://github.com/datajoint/element-lab): lab management related information, such as Lab, User, Project, Protocol, Source."
]
},
{
Expand All @@ -255,19 +267,15 @@
"dj.Diagram(lab)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ [`subject`](https://github.com/datajoint/element-animal): general animal information, such as User, Genetic background."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"title": "[`subject`](https://github.com/datajoint/element-animal): general animal information, such as User, Genetic background."
},
"outputs": [],
"source": [
"\n",
"dj.Diagram(subject)"
]
},
Expand All @@ -282,19 +290,15 @@
"subject.Subject.describe();"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ [`session`](https://github.com/datajoint/element-session): General information of experimental sessions."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"title": "[`session`](https://github.com/datajoint/element-session): General information of experimental sessions."
},
"outputs": [],
"source": [
"\n",
"dj.Diagram(session)"
]
},
Expand All @@ -310,11 +314,14 @@
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"+ [`miniscope`](https://github.com/datajoint/element-miniscope): miniscope raw recording and processed data"
]
"cell_type": "code",
"execution_count": null,
"id": "dc175fed",
"metadata": {
"title": "[`miniscope`](https://github.com/datajoint/element-miniscope): miniscope raw recording and processed data"
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
Expand Down Expand Up @@ -342,7 +349,8 @@
"metadata": {
"jupytext": {
"encoding": "# -*- coding: utf-8 -*-",
"formats": "ipynb,scripts//py"
"formats": "ipynb,scripts//py",
"main_language": "python"
},
"kernelspec": {
"display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",
Expand Down
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