Overhaul tools

[kostrykin]

Todos:

• Check whether skimage.io.imread is capable of reading single-channel PNG files. If not, then tools not capable of dealing with multi-channel images should not be allowed to take png as input. — Yes, it is. To reproduce, use cv2.imwrite to write a single-channel PNG file. It can then be read with skimage.io.imread, although skimage.io.imsave cannot write single-channel PNG files.

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Overhauled tools:

• 2d_auto_threshold
• 2d_feature_extraction
• 2d_filter_segmentation_by_features
• 2d_histogram_equalization
• 2d_simple_filter
• anisotropic_diffusion
• bfconvert
• binary2labelimage
• binaryimage2points
• bioformats2raw
• color-deconvolution
• colorize_labels
• concat_channels
• coordinates_of_roi
• count_objects
• curve_fitting
• detection_viz
• imagecoordinates_flipaxis
• image_info
• image_math
• image_registration_affine
• labelimage2points
• label_to_binary
• landmark_registration
• mahotas-features
• mergeneighboursinlabelimage
• morphological_operations
• orientationpy
• overlay_images
• permutate_axis
• points2binaryimage
• points2labelimage
• points_association_nn
• projective_transformation
• projective_transformation_points
• rfove
• roi2binaryimage
• scale_image
• segmetrics
• slice_image
• split_labelmap
• spot_detection_2d
• superdsm
• unzip
• visceral-evaluatesegmentation
• voronoi_tessellation
• wsi_extract_top_view

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Unmaintained:

• curl_post
• 3d_tensor_feature_dimension_reduction (hidden)

[kostrykin]

Next tool should be scale_image.

• Add option to scale_image and 2d_simple_filter to either preserve the brightness, or preserve the values range. Alternatively, make scale_image and 2d_simple_filter preserve the dtype of the image.
• Add TIFF support to scale_image
• Verify that Pillow cannot read float TIFFs (and check whether we can use tifffile in Galaxy)

[kostrykin]

Todo:

• Add test case with float TIFFs for 2d_simple_filter

Note for upstream PR: The 2d_simple_filter tool now preserves the range of values (a074b7d).

Next tools in line:

• image_math
• morphological_operations
• orientationpy
• split_labelmap

[kostrykin]

Note for upstream PR: The concat_images tool now supports either preserving the range of values or the image brightness (69f59ba).