Added all links, despite missing notebooks, for the future.

doc/source/information/commandline_tools_listing.rst

@@ -35,27 +35,27 @@ Basic image manipulation
 
 	Can be used to create an empty image by example.
 
-.. topic:: medpy_resample.py
+.. topic:: medpy_resample.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_resample.py.ipynb>`_)
 
 	Re-samples an image using b-spline interpolation.
 
-.. topic:: medpy_set_pixel_spacing.py
+.. topic:: medpy_set_pixel_spacing.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_set_pixel_spacing.py.ipynb>`_)
 
 	Manually set the pixel/voxel spacing of an image.
 
 .. topic:: medpy_diff.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_diff.py.ipynb>`_)
 
 	Compares the meta-data and intensity values of two images.
 
-.. topic:: medpy_grid.py
+.. topic:: medpy_grid.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_grid.py.ipynb>`_)
 
 	Creates a binary volume containing a regular grid.
 
-.. topic:: medpy_extract_min_max.py
+.. topic:: medpy_extract_min_max.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_extract_min_max.py.ipynb>`_)
 
 	Extracts the min and max intensity values of one or more images.
 
-.. topic:: medpy_swap_dimensions.py
+.. topic:: medpy_swap_dimensions.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_swap_dimensions.py.ipynb>`_)
 
 	Swap two image dimensions.
 
@@ -70,52 +70,51 @@ Image volume manipulation
 
 	Extracts a sub volume from an image.
 
-.. topic:: medpy_extract_sub_volume_auto.py
+.. topic:: medpy_extract_sub_volume_auto.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_extract_sub_volume_auto.py.ipynb>`_)
 
 	Splits a volume into a number of sub volumes along a given dimension. 
 
 .. topic:: medpy_extract_sub_volume_by_example.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_extract_sub_volume_by_example.py.ipynb>`_)
 
 	Takes an image and a second image containing a binary mask, then extracts the sub volume of the first image defined by the bounding box of the foreground object in the binary image.
 
-.. topic:: medpy_fit_into_shape.py
+.. topic:: medpy_fit_into_shape.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_fit_into_shape.py.ipynb>`_)
 
 	Fit an existing image into a new shape by either extending or cutting all dimensions symmetrically.
 
-.. topic:: medpy_intersection.py
+.. topic:: medpy_intersection.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_intersection.py.ipynb>`_)
 
-  Extracts the intersecting parts of two volumes regarding offset and voxel-
-spacing.	
+  Extracts the intersecting parts of two volumes regarding offset and voxel-spacing.
 
-.. topic:: medpy_join_xd_to_xplus1d.py
+.. topic:: medpy_join_xd_to_xplus1d.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_join_xd_to_xplus1d.py.ipynb>`_)
 
 	Joins a number of xD images by adding a new dimension, resulting in a (x+1)D image.
 
-.. topic:: medpy_split_xd_to_xminus1d.py
+.. topic:: medpy_split_xd_to_xminus1d.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_split_xd_to_xminus1d.py.ipynb>`_)
 
 	Splits a xD image into a number of (x-1)D images.
 
-.. topic:: medpy_stack_sub_volumes.py
+.. topic:: medpy_stack_sub_volumes.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_stack_sub_volumes.py.ipynb>`_)
 
 	Stacks a number of sub volumes together along a defined dimension.
 
-.. topic:: medpy_zoom_image.py
+.. topic:: medpy_zoom_image.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_zoom_image.py.ipynb>`_)
 
 	Enlarges an image by adding (interpolated) slices.
 
-.. topic:: medpy_shrink_image.py
+.. topic:: medpy_shrink_image.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_shrink_image.py.ipynb>`_)
 
 	Reduces an image by simply discarding slices.
 
-.. topic:: medpy_reslice_3d_to_4d.py
+.. topic:: medpy_reslice_3d_to_4d.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_reslice_3d_to_4d.py.ipynb>`_)
 
 	Reslices a 3D image formed by stacked up 3D volumes into a real 4D images (as e.g. often necessary for DICOM).
 
-.. topic:: medpy_dicom_slices_to_volume.py
+.. topic:: medpy_dicom_slices_to_volume.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_dicom_slices_to_volume.py.ipynb>`_)
 
 	Takes a number of 2D DICOM slice (a DICOM series) and creates a 3D volume from them.
 
-.. topic:: medpy_dicom_to_4D.py
+.. topic:: medpy_dicom_to_4D.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_dicom_to_4D.py.ipynb>`_)
 
     Takes a number of 2D DICOM slice (a DICOM series) and creates a 4D volume from them (split-points are passed as arguments).
 
@@ -126,19 +125,19 @@ Binary image manipulation
 =========================
 :ref:`↑top <top>`
 
-.. topic:: medpy_binary_resampling.py
+.. topic:: medpy_binary_resampling.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_binary_resampling.py.ipynb>`_)
 
   Re-samples a binary image according to a supplied voxel spacing using shape based interpolation where necessary.
 
 .. topic:: medpy_extract_contour.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_extract_contour.py.ipynb>`_)
 
   Converts a binary volume into a surface contour.
 
-.. topic:: medpy_join_masks.py
+.. topic:: medpy_join_masks.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_join_masks.py.ipynb>`_)
 
   Joins a number of binary images into a single conjunction using sum, avg, max or min.
 
-.. topic:: medpy_merge.py
+.. topic:: medpy_merge.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_merge.py.ipynb>`_)
 
 	Performs a logical OR on two binary images.
 
@@ -153,7 +152,7 @@ Image filters
 
 	Gradient magnitude image filter. Output is float.
 
-.. topic:: medpy_morphology.py
+.. topic:: medpy_morphology.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_morphology.py.ipynb>`_)
 
 	Apply binary morphology (dilation, erosion, opening or closing) to a binary image.
 
@@ -176,7 +175,7 @@ Magnetic resonance (MR) related
 
 	Computes the apparent diffusion coefficient (ADC) map from two diffusion weight (DW) volumes acquired with different b-values.
 
-.. topic:: medpy_intensity_range_standardization.py
+.. topic:: medpy_intensity_range_standardization.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_intensity_range_standardization.py.ipynb>`_)
 
 	Standardizes the intensity ranges of a number of MR images and produces a corresponding model that can be applied to new images.
 
@@ -197,27 +196,27 @@ GC based on (and shipped with, ask!) Max-flow/min-cut by Boykov-Kolmogorov algor
 
 	Executes a label based graph cut. Only supports the boundary term.
 
-.. topic:: medpy_graphcut_label_bgreduced.py
+.. topic:: medpy_graphcut_label_bgreduced.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_graphcut_label_bgreduced.py.ipynb>`_)
 
 	Executes a label based graph cut. Only supports the boundary term. Reduces the input image by considering only the region defined by the bounding box around the background markers.
 
-.. topic:: medpy_graphcut_label_wsplit.py
+.. topic:: medpy_graphcut_label_wsplit.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_graphcut_label_wsplit.py.ipynb>`_)
 
 	Executes a label based graph cut. Only supports the boundary term. Reduces the memory requirements by splitting the image into a number of sub-volumes. Note that this will result in a non-optimal cut.
 
-.. topic:: medpy_graphcut_label_w_regional.py
+.. topic:: medpy_graphcut_label_w_regional.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_graphcut_label_w_regional.py.ipynb>`_)
 
 	Executes a label based graph cut. With boundary and regional term.
 
-.. topic:: medpy_label_count.py
+.. topic:: medpy_label_count.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_label_count.py.ipynb>`_)
 
 	Counts the number of unique intensity values in an image i.e. the amount of labelled regions.
 
-.. topic:: medpy_label_fit_to_mask.py
+.. topic:: medpy_label_fit_to_mask.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_label_fit_to_mask.py.ipynb>`_)
 
 	Fits the labelled regions of a label map image to a binary segmentation map.
 
-.. topic:: medpy_label_superimposition.py
+.. topic:: medpy_label_superimposition.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_label_superimposition.py.ipynb>`_)
 
 	Takes to label maps and superimpose them to create a new label image with more regions.
 
@@ -230,15 +229,15 @@ Scripts requiring ITK
 
 All of the scripts in this section require the ITK Python bindings to be installed.
 
-.. topic:: medpy_itk_smoothing.py
+.. topic:: medpy_itk_smoothing.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_itk_smoothing.py.ipynb>`_)
 
 	Applies the edge preserving anisotropic diffusion filter to an image.
 
-.. topic:: medpy_itk_gradient.py
+.. topic:: medpy_itk_gradient.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_itk_gradient.py.ipynb>`_)
 
 	Applies a gradient magnitude filter.
 
-.. topic:: medpy_itk_watershed.py
+.. topic:: medpy_itk_watershed.py (`notebook <https://github.com/loli/medpy/blob/master/notebooks/scripts/medpy_itk_watershed.py.ipynb>`_)
 
 	Applies a watershed filter, results in a label map / region image.