# HG changeset patch
# User thomaswollmann
# Date 1546857526 18000
# Node ID e3e4b058db671caf2455079462d162ea10cdbd4d

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f

diff -r 000000000000 -r e3e4b058db67 projective_transformation.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/projective_transformation.py	Mon Jan 07 05:38:46 2019 -0500
@@ -0,0 +1,61 @@
+import skimage.io
+from skimage.transform import ProjectiveTransform
+from scipy.ndimage import map_coordinates
+import numpy as np
+import pandas as pd
+import argparse
+import warnings
+import shutil
+
+
+def _stackcopy(a, b):
+    if a.ndim == 3:
+        a[:] = b[:, :, np.newaxis]
+    else:
+        a[:] = b
+
+
+def warp_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000):
+    rows, cols = shape[0], shape[1]
+    coords_shape = [len(shape), rows, cols]
+    if len(shape) == 3:
+        coords_shape.append(shape[2])
+    coords = np.empty(coords_shape, dtype=dtype)
+
+    tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T
+
+    for i in range(0, (tf_coords.shape[0]//batch_size+1)):
+        tf_coords[batch_size*i:batch_size*(i+1)] = coord_map(tf_coords[batch_size*i:batch_size*(i+1)])
+    tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)
+
+    _stackcopy(coords[1, ...], tf_coords[0, ...])
+    _stackcopy(coords[0, ...], tf_coords[1, ...])
+    if len(shape) == 3:
+        coords[2, ...] = range(shape[2])
+
+    return coords
+
+
+def transform(moving_image, fixed_image, warp_matrix, out):
+    moving_image = skimage.io.imread(moving_image)
+    fixed_image = skimage.io.imread(fixed_image)
+    warp_matrix = pd.read_csv(warp_matrix, delimiter=",", header=None)
+    warp_matrix = np.array(warp_matrix)
+
+    trans = ProjectiveTransform(matrix=warp_matrix)
+    warped_coords = warp_coords_batch(trans, fixed_image.shape)
+    t = map_coordinates(moving_image, warped_coords, mode='reflect')
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        skimage.io.imsave(out, t)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Transform the image")
+    parser.add_argument("fixed_image", help="Paste path to image.png that should be transformed")
+    parser.add_argument("moving_image", help="Paste path to fixed image.png")
+    parser.add_argument("warp_matrix", help="Paste path to warp_matrix.csv that should be used for transformation")
+    parser.add_argument("out", help="Paste path to file in which transformed image should be saved")
+    args = parser.parse_args()
+    transform(args.moving_image, args.fixed_image, args.warp_matrix, args.out)
diff -r 000000000000 -r e3e4b058db67 projective_transformation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/projective_transformation.xml	Mon Jan 07 05:38:46 2019 -0500
@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<tool name="Projective Transformation" id="ip_projective_transformation" version="0.0.4">
+    <description>Projective Transformation</description>
+    <requirements>
+        <requirement type="package" version="0.14.0">scikit-image</requirement>
+        <requirement type="package" version="0.23.4">pandas</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+        <!--<requirement type="package" version="1.1.0">scipy</requirement>-->
+    </requirements>
+    <command>
+    <![CDATA[
+         python '$__tool_directory__/projective_transformation.py'
+         '$fixed_image'
+         '$moving_image'
+         '$warp_matrix'
+         ./out.png
+         && mv ./out.png '$out'
+    ]]>
+    </command>
+    <inputs>
+	<param name="moving_image" type="data" format="png" label="Moving Image" />
+	<param name="fixed_image" type="data" format="png" label="Fixed Image" />
+	<param name="warp_matrix" type= "data" format="csv" label="Warp Matrix" />
+    </inputs>
+    <outputs>
+       <data format="png" name="out" />
+    </outputs>
+    <tests>
+      <test>
+        <param name="fixed_image" value="sample1.png"/>
+        <param name="moving_image" value="sample2.png"/>
+        <param name="warp_matrix" value="warp_matrix.csv"/>
+        <output name="out" value="yam.png" ftype="png" compare="sim_size"/>
+      </test>
+    </tests>
+    <help>
+        This tool performs a projective transformation of the input (moving) image so that it fits the fixed image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r e3e4b058db67 test-data/sample1.png
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diff -r 000000000000 -r e3e4b058db67 test-data/sample2.png
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diff -r 000000000000 -r e3e4b058db67 test-data/warp_matrix.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/warp_matrix.csv	Mon Jan 07 05:38:46 2019 -0500
@@ -0,0 +1,3 @@
+1,0,10
+0,1,20
+0,0,1
diff -r 000000000000 -r e3e4b058db67 test-data/yam.png
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