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DOC: Better document the ipython notebooks #133

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Sep 9, 2021
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DOC: Better document the ipython notebooks #133

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5ff353e
DOC: Better document the ipython notebooks
oesteban Sep 9, 2021
5b7a43c
enh: add prolog and epilog to notebooks
oesteban Sep 9, 2021
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30 changes: 30 additions & 0 deletions docs/conf.py
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Expand Up @@ -222,3 +222,33 @@

# -- Options for versioning extension ----------------------------------------
scv_show_banner = True

nbsphinx_prolog = """
{% set docname = 'docs/' + env.doc2path(env.docname, base=None) %}

.. raw:: html

<div class="admonition note">
This page was generated from
<a class="reference external" href="https://github.com/poldracklab/nitransforms/blob/master\
/{{ docname|e }}">{{ docname|e }}</a>.
<script>
if (document.location.host) {
$(document.currentScript).replaceWith(
'<a class="reference external" ' +
'href="https://nbviewer.jupyter.org/url' +
(window.location.protocol == 'https:' ? 's/' : '/') +
window.location.host +
window.location.pathname.slice(0, -4) +
'ipynb">View in <em>nbviewer</em></a>.'
);
}
</script>
</div>

"""

# This is processed by Jinja2 and inserted after each notebook
nbsphinx_epilog = """
{% set docname = 'docs/notebooks' + env.doc2path(env.docname, base=None) %}
"""
140 changes: 106 additions & 34 deletions docs/notebooks/01_preparing_images.ipynb
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Expand Up @@ -4,7 +4,17 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Preparing images"
"## Preparing images\n",
"\n",
"This notebook uses the example NIfTI from NiBabel's documentation (\"`someones_anatomy.nii.gz`\") and creates several derived versions of it with different orientations, including oblique physical axes (i.e., the physical axes are rotated w.r.t. the canonical axes of the array), ordering of axes (e.g., RSA), and axis flips (e.g., LAS)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Preamble\n",
"Prepare a Python environment and use a temporal directory for the outputs. After that, fetch the actual file from NiBabel documentation."
]
},
{
Expand Down Expand Up @@ -75,6 +85,14 @@
"!wget https://nipy.org/nibabel/_downloads/62985f4c43f499609fa65cb2eb955b79/someones_anatomy.nii.gz"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Load in the image\n",
"Let's first visualize the example image, and retain some copies of the original header and affine."
]
},
{
"cell_type": "code",
"execution_count": 3,
Expand Down Expand Up @@ -112,6 +130,14 @@
"nii.orthoview()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Generating variants\n",
"Playing with the affine header and the data array ordering of axes and elements we generate several versions of the dataset with different orientations (LAS, LPS, oblique, LPS oblique)."
]
},
{
"cell_type": "code",
"execution_count": 4,
Expand Down Expand Up @@ -151,6 +177,15 @@
"lpsnew.to_filename('someones_anatomy_lpsrot.nii.gz')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Quick test with AFNI's `3dWarp -deoblique`\n",
"AFNI `3dWarp` comes with a `-deoblique` option that can be interesting to double check whether the examples above are useful.\n",
"This example checks whether our *oblique* image's version is perceived as such by AFNI, and *realign* it with the canonical axes."
]
},
{
"cell_type": "code",
"execution_count": 28,
Expand All @@ -173,6 +208,13 @@
"!3dWarp -deoblique -prefix deob.nii.gz someones_anatomy_rot.nii.gz"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"AFNI stores the actual rotation matrices of the *deoblique* operation as NIfTI header extensions:"
]
},
{
"cell_type": "code",
"execution_count": 30,
Expand Down Expand Up @@ -419,6 +461,16 @@
"print(nb.load('deob.nii.gz').header.extensions[0].get_content().decode())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Testing the variants with *NiTransforms*, *AFNI*, *ANTs*, and *FSL*, with a rigid-body transform\n",
"Now, let's use these variants to check how they affect in concatenation with other transforms\n",
"\n",
"First, we check that, as *NiBabel* represents the data array disregarding the affine, the `.orthoview()` visualization of the *oblique* image shows the same apparent data orientation as for the original file."
]
},
{
"cell_type": "code",
"execution_count": 5,
Expand Down Expand Up @@ -451,6 +503,13 @@
"new.orthoview()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Create a transform**. We test with a rigid-body transformation with 3 rotations and 3 translations"
]
},
{
"cell_type": "code",
"execution_count": 6,
Expand All @@ -460,6 +519,14 @@
"T = nb.affines.from_matvec(nb.eulerangles.euler2mat(x=0.9, y=0.001, z=0.001), [4.0, 2.0, -1.0])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### *NiTransforms*\n",
"Let's resample the dataset using *NiTransforms*. This result should be similar with the other libraries."
]
},
{
"cell_type": "code",
"execution_count": 7,
Expand Down Expand Up @@ -512,6 +579,13 @@
"moved.orthoview()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Store the transform in other formats**. Let's leverage *NiTransforms*' features to store the transforms for ANTs, FSL, and AFNI."
]
},
{
"cell_type": "code",
"execution_count": 10,
Expand Down Expand Up @@ -544,6 +618,13 @@
"xfm.to_filename('M.afni', moving=new, fmt='afni')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Testing AFNI"
]
},
{
"cell_type": "code",
"execution_count": 24,
Expand Down Expand Up @@ -669,6 +750,13 @@
"moved.orthoview()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Testing ANTs/ITK"
]
},
{
"cell_type": "code",
"execution_count": 13,
Expand Down Expand Up @@ -702,6 +790,13 @@
"nb.load('moved-itk.nii.gz').orthoview()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Testing FSL"
]
},
{
"cell_type": "code",
"execution_count": 14,
Expand Down Expand Up @@ -735,6 +830,14 @@
"nb.load('moved-fsl.nii.gz').orthoview()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Annex: understanding AFNI's deoblique\n",
"The code in this section is just a preamble to the following notebook where we explore how AFNI implemented this operation."
]
},
{
"cell_type": "code",
"execution_count": 35,
Expand Down Expand Up @@ -906,37 +1009,6 @@
"nb.load('moved-afni2.nii.gz').orthoview()\n",
"moved.orthoview()"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"ename": "FileNotFoundError",
"evalue": "No such file or no access: 'moved-RAS.nii.gz'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/workspace/nibabel/nibabel/loadsave.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(filename, **kwargs)\u001b[0m\n\u001b[1;32m 38\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 39\u001b[0;31m \u001b[0mstat_result\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 40\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: 'moved-RAS.nii.gz'",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-31-56fae86f86fd>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mnb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'moved-RAS.nii.gz'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0morthoview\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2\u001b[0m \u001b[0mnb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'moved-affine-oblique-for-T-for.nii.gz'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0morthoview\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mnb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'moved-affine-oblique-for-T-inv.nii.gz'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0morthoview\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/workspace/nibabel/nibabel/loadsave.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(filename, **kwargs)\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0mstat_result\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 40\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mFileNotFoundError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"No such file or no access: '%s'\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 42\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mstat_result\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mst_size\u001b[0m \u001b[0;34m<=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 43\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mImageFileError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Empty file: '%s'\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mFileNotFoundError\u001b[0m: No such file or no access: 'moved-RAS.nii.gz'"
]
}
],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -955,9 +1027,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
"version": "3.8.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
}
32 changes: 29 additions & 3 deletions docs/notebooks/02_afni_deoblique.ipynb
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Expand Up @@ -4,7 +4,12 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## AFNI Deoblique"
"## AFNI Deoblique\n",
"\n",
"This notebook explores the implementation of *deobliquing* operations in AFNI, in order to be able to correctly manipulate transforms generated by the tool, and to produce transforms that can be correctly applied with AFNI.\n",
"Most of the preparation comes from the previous notebook.\n",
"\n",
"### Preparation"
]
},
{
Expand Down Expand Up @@ -199,6 +204,13 @@
"print(np.linalg.inv(np.diag([-1, -1, 1, 1]).dot(R)).T)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Run `3dWarp -deoblique`"
]
},
{
"cell_type": "code",
"execution_count": 81,
Expand Down Expand Up @@ -286,6 +298,13 @@
" return matvec_inv"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Inspecting affines and headers"
]
},
{
"cell_type": "code",
"execution_count": 209,
Expand Down Expand Up @@ -1020,6 +1039,13 @@
"print(deob.header.extensions[0].get_content().decode())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Reverse-engineering matrix compositions of oblique datasets"
]
},
{
"cell_type": "code",
"execution_count": 38,
Expand Down Expand Up @@ -1183,9 +1209,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
"version": "3.8.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
}