diff --git a/.gitignore b/.gitignore index 40f5059..858d79a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ .coverage +.ipynb_checkpoints/ build/ dist/ version.py diff --git a/examples/Pipfile b/examples/Pipfile index 5316de0..32031d5 100644 --- a/examples/Pipfile +++ b/examples/Pipfile @@ -5,12 +5,13 @@ name = "pypi" [packages] freesurfer-volume-reader = {editable = true, path = "./.."} -pandas = "*" -matplotlib = "*" -seaborn = "*" +pandas = "<1" +matplotlib = "<4" +seaborn = "<1" +notebook = "<6" [dev-packages] -pylint = ">=2.3.0" +pylint = ">=2.3.0,<3" [requires] python_version = "3" diff --git a/examples/Pipfile.lock b/examples/Pipfile.lock index e67aed0..5236f49 100644 --- a/examples/Pipfile.lock +++ b/examples/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "94e40b19654a4b576025e3b71130118fbc55f3b7f00faeab681d96d3cd356500" + "sha256": "44af26c0d569cb35ce1fe22948c430ebe601c355048b513cc35f39f54a5960ab" }, "pipfile-spec": 6, "requires": { @@ -16,6 +16,27 @@ 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"markers": "implementation_name == 'cpython'", - "version": "==1.3.4" + "version": "==1.3.5" }, "wrapt": { "hashes": [ diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000..1729fc9 --- /dev/null +++ b/examples/README.md @@ -0,0 +1,12 @@ +# freesurfer-volume-reader examples + +View examples online with jupyter's +[nbviewer](https://nbviewer.jupyter.org/github/fphammerle/freesurfer-volume-reader/tree/master/examples/) + +or locally: +```sh +pip3 install --user pipenv +git clone https://github.com/fphammerle/freesurfer-volume-reader.git +cd freesurfer-volume-reader/examples +pipenv run jupyter notebook +``` diff --git a/examples/ashs.ipynb b/examples/ashs.ipynb new file mode 100644 index 0000000..40247f9 --- /dev/null +++ b/examples/ashs.ipynb @@ -0,0 +1,1141 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# ASHS" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "SUBJECTS_DIR = '../tests/subjects'\n", + "SUBJECT = 'bert'" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['bert_right_corr_nogray_volumes.txt',\n", + " 'bert_left_heur_volumes.txt',\n", + " 'bert_left_corr_usegray_volumes.txt',\n", + " 'bert_left_corr_nogray_volumes.txt']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import os\n", + "from freesurfer_volume_reader.ashs import HippocampalSubfieldsVolumeFile\n", + "\n", + "volume_files = list(filter(lambda f: f.subject == SUBJECT, \n", + " HippocampalSubfieldsVolumeFile.find(SUBJECTS_DIR)))\n", + "[os.path.basename(f.absolute_path) for f in volume_files]" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " subfield volume_mm^3 subject hemisphere correction\n", + "0 CA1 678.903 bert right nogray\n", + "1 CA2+3 123.458 bert right nogray\n", + "2 DG 901.236 bert right nogray\n", + "3 ERC 789.013 bert right nogray\n", + "4 PHC 2345.878 bert right nogray" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas\n", + "volume_frame = pandas.concat([f.read_volumes_dataframe() for f in volume_files])\n", + "volume_frame.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "nogray 14\n", + "usegray 7\n", + "none 7\n", + "Name: correction, dtype: int64" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "volume_frame['correction'].fillna('none', inplace=True)\n", + "volume_frame['correction'].value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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