Merge pull request #59 from plaresmedima/development

update docs
QIB-Sheffield · Dec 3, 2024 · dad40b6 · dad40b6
2 parents f672c4e + 0ff7e19
commit dad40b6
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diff --git a/dev/sops.txt b/dev/sops.txt
@@ -103,7 +103,7 @@ Building release notes
 - Save the token in the environment variable GH_TOKEN. On windows:
 >>> $env:GH_TOKEN='token'
 - Build the changelog from current version to current dev. For instance:
->>> changelist QIB-Sheffield/mdreg 0.4.0 dev --format rst
+>>> changelist QIB-Sheffield/mdreg 0.4.0 development --format rst
 - Copy-paste the terminal output in an .rst file and save it in docs/source/releases
 - Edit the content of the file manually as needed
 - Add an entry in the index of docs/source/releases

diff --git a/...ples/use_cases/plot_poor_model_fitting.py → ...les/use_cases/_plot_poor_model_fitting.py b/...ples/use_cases/plot_poor_model_fitting.py → ...les/use_cases/_plot_poor_model_fitting.py
@@ -18,7 +18,7 @@
 
 #%% 
 # Import packages and data
-# ----------------------------
+# ------------------------
 # Example data can be easily loaded in using the `fetch` function.
 
 import numpy as np
@@ -31,14 +31,14 @@
 
 #%% 
 # Extract the desired slice from the data array
-# ----------------------------
+# ---------------------------------------------
 # As an intial step, we will extract the 4D data (x,y,z,t) from the fetched data dictionary.
 
 array = data['array']
 
 #%%
 # Signal model theory
-# ----------------------------
+# -------------------
 # The signal model used in this example is the non-linear variable flip angle 
 # SPGR model. The signal model is defined by the following equation:
 #
@@ -52,7 +52,7 @@
 
 #%%
 # Define model fit parameters
-# ----------------------------
+# ---------------------------
 # The image fitting settings dictionary (`vfa_fit` in this case) is required by 
 # `mdreg.fit` to fit a specific signal model to the data. Leaving this as None 
 # will fit a constant model to the data as a default.
@@ -71,7 +71,7 @@
 
 #%%
 # Define the coregistration parameters
-# ----------------------------
+# ------------------------------------
 # The coregistration parameters are set in the `coreg_params` dictionary.
 # The `package` key specifies the coregistration package to be used, with a 
 # choice of elastix, skimage, or dipy.
@@ -91,7 +91,7 @@
 
 #%%
 # Define the plotting parameters
-# ----------------------------
+# ------------------------------
 # The plotting parameters are set in the `plot_settings` dictionary.
 #
 # The `interval` key specifies the time interval between frames in 
@@ -121,7 +121,7 @@
 
 #%% 
 # Perform model-driven coregistration
-# ----------------------------
+# -----------------------------------
 # The `mdreg.fit` function is used to perform the model-driven coregistration.
 # The function requires the 4D data array, the fit_image dictionary, and the 
 # coregistration parameters we have already defined.
@@ -142,7 +142,7 @@
 
 #%% 
 # Visualise coregistration results
-# ---------------------------------
+# --------------------------------
 # To easily visualise the output of the employ the `mdreg.plot` module to 
 # easily produce animations that render on screen or save as a gif.
 # Here we utilise `mdreg.plot_series` which accepts both 2D and 3D spatial data 
@@ -167,7 +167,7 @@
 
 #%% 
 # Export all series at once
-# ----------------------------
+# -------------------------
 # The `mdreg.plot_series` function can be used to plot the original, fitted and
 # coregistered data for all slices in the data array. This function can also
 # be used to save the animations to a file. 
@@ -178,7 +178,7 @@
 #  >>> anims = mdreg.plot_series(array, fit, coreg, **plot_settings)
 
 #%% 
-# Identifiying poor model fitting
+# Identifying poor model fitting
 # ------------------------------
 # 
 # The coregistration results show significant defects in the coregistered data.
@@ -256,7 +256,7 @@
 
 #%%
 # Goodness of fit
-# ----------------------------
+# ---------------
 # The chi squared values in the figure above show large regions of poor fit
 # across the data array. These regions are highlighted in red as above the 99th
 # percentile of the chi squared values. These region also correspond to the 

diff --git a/docs/examples/use_cases/deformationField.mhd b/docs/examples/use_cases/deformationField.mhd
@@ -0,0 +1,14 @@
+ObjectType = Image
+NDims = 3
+BinaryData = True
+BinaryDataByteOrderMSB = False
+CompressedData = False
+TransformMatrix = 1 0 0 0 1 0 0 0 1
+Offset = 0 0 0
+CenterOfRotation = 0 0 0
+AnatomicalOrientation = RAI
+ElementSpacing = 5 4.6875 4.6875
+DimSize = 36 96 78
+ElementNumberOfChannels = 3
+ElementType = MET_FLOAT
+ElementDataFile = deformationField.raw
diff --git a/docs/examples/use_cases/deformationField.raw b/docs/examples/use_cases/deformationField.raw
diff --git a/docs/examples/use_cases/plot_3Dexample_vfa.py b/docs/examples/use_cases/plot_3Dexample_vfa.py
@@ -13,7 +13,7 @@
 
 #%% 
 # Import packages and data
-# ----------------------------
+# ------------------------
 # Example data can be easily loaded in using the `fetch` function.
 
 import numpy as np
@@ -24,15 +24,15 @@
 
 #%% 
 # Extract the desired slice from the data array
-# ----------------------------
+# ---------------------------------------------
 # As an intial step, we will extract the 4D data (x,y,z,t) from the fetched 
 # data dictionary.
 
 array = data['array']
 
 #%%
 # Signal model theory
-# ----------------------------
+# -------------------
 # The signal model used in this example is the variable flip angle 
 # SPGR model. The signal model is defined by the following equation:
 #
@@ -64,7 +64,7 @@
 
 #%%
 # Define model fit parameters
-# ----------------------------
+# ---------------------------
 # The image fitting settings dictionary (`vfa_fit` in this case) is 
 # required by `mdreg.fit` to fit a specific signal model to the data. Leaving 
 # this as None will fit a constant model to the data as a default.
@@ -80,7 +80,7 @@
     }
 #%%
 # Define the coregistration parameters
-# ----------------------------
+# ------------------------------------
 # The coregistration parameters are set in the `coreg_params` dictionary.
 # The `package` key specifies the coregistration package to be used, with a 
 # choice of elastix, skimage, or dipy.
@@ -99,7 +99,7 @@
 
 #%%
 # Define the plotting parameters
-# ----------------------------
+# ------------------------------
 # The plotting parameters are set in the `plot_settings` dictionary.
 #
 # The `interval` key specifies the time interval between frames in 
@@ -136,7 +136,7 @@
 
 #%% 
 # Perform model-driven coregistration
-# ----------------------------
+# -----------------------------------
 # The `mdreg.fit` function is used to perform the model-driven coregistration.
 # The function requires the 4D data array, the fit_image dictionary, and the 
 # coregistration parameters we have already defined.
@@ -158,7 +158,7 @@
 
 #%% 
 # Visualize the results
-# ----------------------------
+# ---------------------
 # To easily visualise the output of the employ the `mdreg.plot` module to 
 # easily produce animations that render on screen or save as a gif.
 # Here we utilise `mdreg.plot_series` which accepts both 2D and 3D spatial data 
@@ -179,7 +179,7 @@
 
 #%% 
 # Export all series at once
-# ----------------------------
+# -------------------------
 # The `mdreg.plot_series` function can be used to plot the original, fitted and
 # coregistered data for all slices in the data array. This function can also
 # be used to save the animations to a file. 

diff --git a/docs/source/generated/backreferences/mdreg.animation.examples b/docs/source/generated/backreferences/mdreg.animation.examples
@@ -15,24 +15,24 @@ Examples using ``mdreg.animation``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="By default, dcmri uses free-form deformation implemented in the package  itk.elastix, which default settings for all configuration parameters. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the effect of poor model fitting on coregistration for the 3D Variable Flip Angle (VFA) dataset used in the 3D data example.">
 
 .. only:: html
 
-  .. image:: /generated/examples/tutorials/images/thumb/sphx_glr_plot_getting_started_defo_thumb.gif
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">Customizing the coregistration</div>
+      <div class="sphx-glr-thumbnail-title">Example: Poor Model Fitting</div>
     </div>
 
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close
 

diff --git a/docs/source/generated/backreferences/mdreg.elastix.params.examples b/docs/source/generated/backreferences/mdreg.elastix.params.examples
@@ -15,24 +15,24 @@ Examples using ``mdreg.elastix.params``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="By default, dcmri uses free-form deformation implemented in the package  itk.elastix, which default settings for all configuration parameters. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the effect of poor model fitting on coregistration for the 3D Variable Flip Angle (VFA) dataset used in the 3D data example.">
 
 .. only:: html
 
-  .. image:: /generated/examples/tutorials/images/thumb/sphx_glr_plot_getting_started_defo_thumb.gif
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">Customizing the coregistration</div>
+      <div class="sphx-glr-thumbnail-title">Example: Poor Model Fitting</div>
     </div>
 
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close
 

diff --git a/docs/source/generated/backreferences/mdreg.fetch.examples b/docs/source/generated/backreferences/mdreg.fetch.examples
@@ -15,24 +15,24 @@ Examples using ``mdreg.fetch``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="By default, dcmri uses free-form deformation implemented in the package  itk.elastix, which default settings for all configuration parameters. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the effect of poor model fitting on coregistration for the 3D Variable Flip Angle (VFA) dataset used in the 3D data example.">
 
 .. only:: html
 
-  .. image:: /generated/examples/tutorials/images/thumb/sphx_glr_plot_getting_started_defo_thumb.gif
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">Customizing the coregistration</div>
+      <div class="sphx-glr-thumbnail-title">Example: Poor Model Fitting</div>
     </div>
 
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close
 

diff --git a/docs/source/generated/backreferences/mdreg.fit.examples b/docs/source/generated/backreferences/mdreg.fit.examples
@@ -15,24 +15,24 @@ Examples using ``mdreg.fit``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="By default, dcmri uses free-form deformation implemented in the package  itk.elastix, which default settings for all configuration parameters. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the effect of poor model fitting on coregistration for the 3D Variable Flip Angle (VFA) dataset used in the 3D data example.">
 
 .. only:: html
 
-  .. image:: /generated/examples/tutorials/images/thumb/sphx_glr_plot_getting_started_defo_thumb.gif
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">Customizing the coregistration</div>
+      <div class="sphx-glr-thumbnail-title">Example: Poor Model Fitting</div>
     </div>
 
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close
 

diff --git a/docs/source/generated/backreferences/mdreg.plot.examples b/docs/source/generated/backreferences/mdreg.plot.examples
@@ -19,10 +19,10 @@ Examples using ``mdreg.plot``
 
 .. only:: html
 
-  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr_plot_poor_model_fitting_thumb.png
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_use_cases_plot_poor_model_fitting.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
@@ -32,7 +32,7 @@ Examples using ``mdreg.plot``
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_use_cases_plot_poor_model_fitting.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close
 

diff --git a/docs/source/generated/backreferences/mdreg.plot_series.examples b/docs/source/generated/backreferences/mdreg.plot_series.examples
@@ -15,24 +15,24 @@ Examples using ``mdreg.plot_series``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="By default, dcmri uses free-form deformation implemented in the package  itk.elastix, which default settings for all configuration parameters. ">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates the effect of poor model fitting on coregistration for the 3D Variable Flip Angle (VFA) dataset used in the 3D data example.">
 
 .. only:: html
 
-  .. image:: /generated/examples/tutorials/images/thumb/sphx_glr_plot_getting_started_defo_thumb.gif
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
-      <div class="sphx-glr-thumbnail-title">Customizing the coregistration</div>
+      <div class="sphx-glr-thumbnail-title">Example: Poor Model Fitting</div>
     </div>
 
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_tutorials_plot_getting_started_defo.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close
 

diff --git a/docs/source/generated/backreferences/mdreg.spgr_vfa_nonlin.examples b/docs/source/generated/backreferences/mdreg.spgr_vfa_nonlin.examples
@@ -19,10 +19,10 @@ Examples using ``mdreg.spgr_vfa_nonlin``
 
 .. only:: html
 
-  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr_plot_poor_model_fitting_thumb.png
+  .. image:: /generated/examples/use_cases/images/thumb/sphx_glr__plot_poor_model_fitting_thumb.png
     :alt:
 
-  :ref:`sphx_glr_generated_examples_use_cases_plot_poor_model_fitting.py`
+  :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. raw:: html
 
@@ -32,7 +32,7 @@ Examples using ``mdreg.spgr_vfa_nonlin``
 
 .. only:: not html
 
- * :ref:`sphx_glr_generated_examples_use_cases_plot_poor_model_fitting.py`
+ * :ref:`sphx_glr_generated_examples_use_cases__plot_poor_model_fitting.py`
 
 .. thumbnail-parent-div-close