From a6713c9ff6be8f5855bbd64aa57d8e46e0cfedb3 Mon Sep 17 00:00:00 2001 From: loli Date: Wed, 20 Sep 2017 18:41:52 +0200 Subject: [PATCH] Added all links, despite missing notebooks, for the future. --- .../information/commandline_tools_listing.rst | 63 +++++++++---------- 1 file changed, 31 insertions(+), 32 deletions(-) diff --git a/doc/source/information/commandline_tools_listing.rst b/doc/source/information/commandline_tools_listing.rst index 309d8753..841695e5 100644 --- a/doc/source/information/commandline_tools_listing.rst +++ b/doc/source/information/commandline_tools_listing.rst @@ -35,11 +35,11 @@ Basic image manipulation Can be used to create an empty image by example. -.. topic:: medpy_resample.py +.. topic:: medpy_resample.py (`notebook `_) Re-samples an image using b-spline interpolation. -.. topic:: medpy_set_pixel_spacing.py +.. topic:: medpy_set_pixel_spacing.py (`notebook `_) Manually set the pixel/voxel spacing of an image. @@ -47,15 +47,15 @@ Basic image manipulation Compares the meta-data and intensity values of two images. -.. topic:: medpy_grid.py +.. topic:: medpy_grid.py (`notebook `_) Creates a binary volume containing a regular grid. -.. topic:: medpy_extract_min_max.py +.. topic:: medpy_extract_min_max.py (`notebook `_) Extracts the min and max intensity values of one or more images. -.. topic:: medpy_swap_dimensions.py +.. topic:: medpy_swap_dimensions.py (`notebook `_) Swap two image dimensions. @@ -70,7 +70,7 @@ 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 `_) Splits a volume into a number of sub volumes along a given dimension. @@ -78,44 +78,43 @@ Image volume manipulation 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 `_) 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 `_) - 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 `_) 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 `_) 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 `_) Stacks a number of sub volumes together along a defined dimension. -.. topic:: medpy_zoom_image.py +.. topic:: medpy_zoom_image.py (`notebook `_) Enlarges an image by adding (interpolated) slices. -.. topic:: medpy_shrink_image.py +.. topic:: medpy_shrink_image.py (`notebook `_) Reduces an image by simply discarding slices. -.. topic:: medpy_reslice_3d_to_4d.py +.. topic:: medpy_reslice_3d_to_4d.py (`notebook `_) 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 `_) 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 `_) Takes a number of 2D DICOM slice (a DICOM series) and creates a 4D volume from them (split-points are passed as arguments). @@ -126,7 +125,7 @@ Binary image manipulation ========================= :ref:`↑top ` -.. topic:: medpy_binary_resampling.py +.. topic:: medpy_binary_resampling.py (`notebook `_) Re-samples a binary image according to a supplied voxel spacing using shape based interpolation where necessary. @@ -134,11 +133,11 @@ Binary image manipulation Converts a binary volume into a surface contour. -.. topic:: medpy_join_masks.py +.. topic:: medpy_join_masks.py (`notebook `_) 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 `_) 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 `_) 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 `_) 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 `_) 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 `_) 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 `_) Executes a label based graph cut. With boundary and regional term. -.. topic:: medpy_label_count.py +.. topic:: medpy_label_count.py (`notebook `_) 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 `_) 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 `_) 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 `_) Applies the edge preserving anisotropic diffusion filter to an image. -.. topic:: medpy_itk_gradient.py +.. topic:: medpy_itk_gradient.py (`notebook `_) Applies a gradient magnitude filter. -.. topic:: medpy_itk_watershed.py +.. topic:: medpy_itk_watershed.py (`notebook `_) Applies a watershed filter, results in a label map / region image.