enh: finishing the transforms module

Adds a bunch of notebooks about coordinates, affines and nonlinear
transforms to the jupyter book.

_config.yml

@@ -22,86 +22,93 @@ exclude_patterns:
   # string_formatting.Rmd.
   # https://github.com/executablebooks/meta/discussions/105
   # https://myst-nb.readthedocs.io/en/latest/use/orphaned_nb.html#orphaned-nb
-  - README.md
-  - todo.md
-  - _scripts
+  # OE: I have sorted the pages with a tentative sectioning
+  #
+  # Python and Numpy
   - pages/allclose.Rmd
-  - pages/anterior_cingulate.md
   - pages/arange.Rmd
-  - pages/array_reductions.md
-  - pages/bibliography.md
   - pages/boolean_indexing.Rmd
-  - pages/choosing_editor.md
-  - pages/classes.md
-  - pages/classes_and_labs.md
-  - pages/coding_style.md
+  - pages/array_reductions.md
   - pages/comparing_arrays.Rmd
   - pages/comparing_floats.md
   - pages/diag_inverse.md
-  - pages/diagnostics_project.md
-  - pages/dipy_registration.Rmd
   - pages/docstrings.md
   - pages/dot_and_outer.md
   - pages/dot_outer.Rmd
-  - pages/ds114_sub009_highres.nii
-  - pages/example_data.md
-  - pages/exercises.md
   - pages/floating_in_text.md
+  - pages/index_reshape.Rmd
+  - pages/keyword_arguments.Rmd
+  - pages/list_comprehensions.Rmd
+  - pages/methods_vs_functions.Rmd
+  - pages/nans.md
+  - pages/newaxis.Rmd
+  - pages/numpy_diag.Rmd
+  - pages/numpy_meshgrid.Rmd
+  - pages/numpy_random.Rmd
+  - pages/numpy_squeeze.Rmd
+  - pages/numpy_transpose.Rmd
+  - pages/on_loops.Rmd
+  - pages/packages_namespaces.Rmd
+  - pages/printing_floating.Rmd
+  - pages/string_literals.md
+  - pages/subtract_mean_math.md
+  - pages/subtract_means.Rmd
+  - pages/two_dunders.md
+  # Images and code and images
+  - pages/saving_images.Rmd
+  - pages/plot_lines.Rmd
+  - pages/subplots.Rmd
+  # Coordinate systems and spatial transforms
+  # [all transferred already]
+  # Into the fourth dimension
+  - pages/reshape_and_4d.Rmd
+  - pages/tr_and_headers.Rmd
+  # Statistics
+  - pages/whole_image_statistics.Rmd
+  - pages/pearson_functions.md
+  - pages/validate_against_scipy.Rmd
+  # Hemodynamic response modeling
+  - pages/anterior_cingulate.md
+  - pages/otsu_threshold.Rmd
+  - pages/introducing_nipype.Rmd
+  # Code organization and collaboration
+  - pages/choosing_editor.md
+  - pages/coding_style.md
   - pages/full_scripting.md
   - pages/git_videos.md
   - pages/git_walk_through.Rmd
   - pages/git_workflow_exercises.md
   - pages/github_dummies_homework.md
   - pages/github_glm_homework.md
   - pages/github_pca_homework.md
-  - pages/glossary.md
-  - pages/image_header_and_affine.Rmd
-  - pages/images_and_affines.Rmd
-  - pages/index.md
-  - pages/index_reshape.Rmd
   - pages/installation_on_linux.md
   - pages/installation_on_mac.md
   - pages/installation_on_windows.md
-  - pages/introducing_nipype.Rmd
-  - pages/keyword_arguments.Rmd
-  - pages/list_comprehensions.Rmd
+  # Meta-course
+  - README.md
+  - todo.md
+  - _scripts
+  - pages/bibliography.md
+  - pages/classes.md
+  - pages/classes_and_labs.md
+  - pages/diagnostics_project.md
+  - pages/ds114_sub009_highres.nii
+  - pages/example_data.md
+  - pages/exercises.md
+  - pages/glossary.md
+  - pages/index.md
   - pages/logistics.md
   - pages/markdown.md
   - pages/mentors.md
-  - pages/methods_vs_functions.Rmd
   - pages/multi_model_homework.md
-  - pages/nans.md
-  - pages/newaxis.Rmd
-  - pages/numpy_diag.Rmd
-  - pages/numpy_meshgrid.Rmd
-  - pages/numpy_random.Rmd
-  - pages/numpy_squeeze.Rmd
-  - pages/numpy_transpose.Rmd
-  - pages/on_loops.Rmd
-  - pages/otsu_threshold.Rmd
-  - pages/packages_namespaces.Rmd
   - pages/participate.md
   - pages/participate_grading.md
-  - pages/pearson_functions.md
-  - pages/plot_lines.Rmd
   - pages/preparation.md
-  - pages/printing_floating.Rmd
   - pages/project_grading.md
   - pages/projects.md
-  - pages/resampling_with_ndimage.Rmd
-  - pages/reshape_and_4d.Rmd
-  - pages/rotation_2d_3d.md
-  - pages/saving_images.Rmd
-  - pages/string_literals.md
-  - pages/subplots.Rmd
-  - pages/subtract_mean_math.md
-  - pages/subtract_means.Rmd
   - pages/topics.md
-  - pages/tr_and_headers.Rmd
-  - pages/two_dunders.md
+  # Drop?
   - pages/using_pythonpath.Rmd
-  - pages/validate_against_scipy.Rmd
-  - pages/whole_image_statistics.Rmd
 
 # Define the name of the latex output file for PDF builds
 latex:

_toc.yml

@@ -26,6 +26,11 @@ parts:
   - file: pages/nibabel_affines
   - file: pages/nibabel_apply_affine
   - file: pages/map_coordinates
+  - file: pages/image_header_and_affine
+  - file: pages/images_and_affines
+  - file: pages/rotation_2d_3d
+  - file: pages/resampling_with_ndimage
+  - file: pages/dipy_registration
 - caption: Statistics
   chapters:
   - file: pages/mean_test_example

code/rotations.py

@@ -0,0 +1,66 @@
+""" Rotation matrices for rotations around x, y, z axes
+
+See: https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+"""
+
+import numpy as np
+
+
+def x_rotmat(theta):
+    """ Rotation matrix for rotation of `theta` radians around x axis
+
+    Parameters
+    ----------
+    theta : scalar
+        Rotation angle in radians
+
+    Returns
+    -------
+    M : shape (3, 3) array
+        Rotation matrix
+    """
+    cos_t = np.cos(theta)
+    sin_t = np.sin(theta)
+    return np.array([[1, 0, 0],
+                     [0, cos_t, -sin_t],
+                     [0, sin_t, cos_t]])
+
+
+def y_rotmat(theta):
+    """ Rotation matrix for rotation of `theta` radians around y axis
+
+    Parameters
+    ----------
+    theta : scalar
+        Rotation angle in radians
+
+    Returns
+    -------
+    M : shape (3, 3) array
+        Rotation matrix
+    """
+    cos_t = np.cos(theta)
+    sin_t = np.sin(theta)
+    return np.array([[cos_t, 0, sin_t],
+                     [0, 1, 0],
+                     [-sin_t, 0, cos_t]])
+
+
+def z_rotmat(theta):
+    """ Rotation matrix for rotation of `theta` radians around z axis
+
+    Parameters
+    ----------
+    theta : scalar
+        Rotation angle in radians
+
+    Returns
+    -------
+    M : shape (3, 3) array
+        Rotation matrix
+    """
+    cos_t = np.cos(theta)
+    sin_t = np.sin(theta)
+    return np.array([[cos_t, -sin_t, 0],
+                     [sin_t, cos_t, 0],
+                     [0, 0, 1]])

pages/dipy_registration.Rmd

@@ -6,11 +6,13 @@ jupyter:
       format_name: rmarkdown
       format_version: '1.2'
       jupytext_version: 1.11.5
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 
-$\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}$
-
-## Registration with dipy
+# Registration with dipy
 
 [Dipy](http://nipy.org/dipy) is a Python package for diffusion imaging.
 
@@ -86,9 +88,9 @@ Dipy works on the image data arrays. It also needs the affine arrays of each
 of the images:
 
 ```{python}
-moving_data = moving_img.get_data()
+moving_data = moving_img.get_fdata()
 moving_affine = moving_img.affine
-template_data = template_img.get_data()
+template_data = template_img.get_fdata()
 template_affine = template_img.affine
 ```
 
@@ -262,31 +264,3 @@ regtools.overlay_slices(template_data, warped_moving, None, 1,
 regtools.overlay_slices(template_data, warped_moving, None, 2,
                         "Template", "Transformed")
 ```
-
-<!-- vim:ft=rst -->
-<!-- Course -->
-<!-- BIC -->
-<!-- Python distributions -->
-<!-- Version control -->
-<!-- Editors -->
-<!-- Python and common libraries -->
-<!-- IPython -->
-<!-- Virtualenv and helpers -->
-<!-- Pypi and packaging -->
-<!-- Mac development -->
-<!-- Windows development -->
-<!-- Nipy and friends -->
-<!-- FMRI datasets -->
-<!-- Languages -->
-<!-- Imaging software -->
-<!-- Installation -->
-<!-- Tutorials -->
-<!-- MB tutorials -->
-<!-- Ideas -->
-<!-- Psych-214 -->
-<!-- People -->
-<!-- Licenses -->
-<!-- Neuroimaging stuff -->
-<!-- OpenFMRI projects -->
-<!-- Unix -->
-<!-- Substitutions -->

pages/ds107_sub012_highres.nii

@@ -0,0 +1 @@
+../data/ds107_sub012_highres.nii

pages/ds114_sub009_highres_brain_222.nii

@@ -0,0 +1 @@
+../data/ds114_sub009_highres_brain_222.nii

pages/ds114_sub009_highres_moved.hdr

@@ -0,0 +1 @@
+../data/ds114_sub009_highres_moved.hdr

pages/ds114_sub009_highres_moved.img

@@ -0,0 +1 @@
+../data/ds114_sub009_highres_moved.img

pages/image_header_and_affine.Rmd

@@ -6,25 +6,20 @@ jupyter:
       format_name: rmarkdown
       format_version: '1.2'
       jupytext_version: 1.11.5
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 
-$\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}$
-
-## The image header and affine
+# The image header and affine
 
 See: [coordinate systems and affine transforms](http://nipy.org/nibabel/coordinate_systems.html) for an introduction.
 
 ```{python}
 # import common modules
 import numpy as np
 np.set_printoptions(precision=4, suppress=True)  # print arrays to 4DP
-import matplotlib.pyplot as plt
-```
-
-```{python}
-#: gray colormap and nearest neighbor interpolation by default
-plt.rcParams['image.cmap'] = 'gray'
-plt.rcParams['image.interpolation'] = 'nearest'
 ```
 
 ## The image affine
@@ -87,31 +82,3 @@ may still find them used. They have only one advantage, which is that, if some
 software wants to change only the header information, it only has to rewrite a
 small `.hdr` file, rather than the whole `.nii` file containing the image
 data and the header.
-
-<!-- vim:ft=rst -->
-<!-- Course -->
-<!-- BIC -->
-<!-- Python distributions -->
-<!-- Version control -->
-<!-- Editors -->
-<!-- Python and common libraries -->
-<!-- IPython -->
-<!-- Virtualenv and helpers -->
-<!-- Pypi and packaging -->
-<!-- Mac development -->
-<!-- Windows development -->
-<!-- Nipy and friends -->
-<!-- FMRI datasets -->
-<!-- Languages -->
-<!-- Imaging software -->
-<!-- Installation -->
-<!-- Tutorials -->
-<!-- MB tutorials -->
-<!-- Ideas -->
-<!-- Psych-214 -->
-<!-- People -->
-<!-- Licenses -->
-<!-- Neuroimaging stuff -->
-<!-- OpenFMRI projects -->
-<!-- Unix -->
-<!-- Substitutions -->