Mercurial > repos > iuc > imagej2_bunwarpj_raw_transform

changeset 1:0ff301860507 draft

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planemo upload commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author iuc
date Fri, 26 Jun 2015 05:29:00 -0400
parents 64aacdf3171f
children 6f129c1ec6d1
files imagej2_base_utils.py imagej2_bunwarpj_raw_transform.py imagej2_bunwarpj_raw_transform.xml imagej2_macros.xml
diffstat 4 files changed, 32 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/imagej2_base_utils.py	Fri Jun 19 16:59:58 2015 -0400
+++ b/imagej2_base_utils.py	Fri Jun 26 05:29:00 2015 -0400
@@ -95,7 +95,7 @@
     if max_heap_size_type == 'default':
         return None
     if max_heap_size_type == 'megabytes':
-        if max_heap_size % 1024 not in [ 0, 256, 512 ]:
+        if int( max_heap_size ) % 1024 not in [ 0, 256, 512 ]:
             return None
         return '%sm' % str( max_heap_size )
     if max_heap_size_type == 'gigabytes':
--- a/imagej2_bunwarpj_raw_transform.py	Fri Jun 19 16:59:58 2015 -0400
+++ b/imagej2_bunwarpj_raw_transform.py	Fri Jun 26 05:29:00 2015 -0400
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 import argparse
-import os
 import shutil
 import subprocess
 import tempfile
@@ -12,7 +11,7 @@
 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--raw_transformation', dest='raw_transformation', default=None, help='Raw transformation as saved by bUnwarpJ' )
+parser.add_argument( '--raw_transformation', dest='raw_transformation', help='Raw transformation as saved by bUnwarpJ' )
 parser.add_argument( '--source_out', help='Output source image' )
 parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
--- a/imagej2_bunwarpj_raw_transform.xml	Fri Jun 19 16:59:58 2015 -0400
+++ b/imagej2_bunwarpj_raw_transform.xml	Fri Jun 26 05:29:00 2015 -0400
@@ -16,8 +16,7 @@
     --source_out "$source_out"
     --source_out_datatype $source_out_datatype
     --jython_script $__tool_directory__/jython_script.py
-    --max_heap_size_type $set_max_heap_size.max_heap_size_type
-    --max_heap_size $set_max_heap_size.max_heap_size
+    @max_heap_size_args@
 ]]>
     </command>
     <inputs>
@@ -59,25 +58,5 @@
 ]]>
 
     </help>
-    <citations>
-        <citation type="bibtex">
-            @InProceedings(Arganda-Carreras2006,
-                author =     "Ignacio Arganda-Carreras and
-                                    Carlos Oscar S{\'a}nchez Sorzano and
-                                    Roberto Marabini and
-                                    Jos{\'e} Mar\'{\i}a Carazo and
-                                    Carlos Ortiz-de-Solorzano and
-                                    Jan Kybic",
-                title =          "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",    
-                publisher =  "Springer Berlin / Heidelberg",    
-                booktitle =   "Computer Vision Approaches to Medical Image Analysis",
-                series =       "Lecture Notes in Computer Science",
-                year =          "2006",
-                volume =      "4241",
-                pages =       "85-95",
-                month =       "May",
-                city =            "Graz, Austria")
-        </citation>
-        <citation type="doi">10.1038/nmeth.2019</citation>
-    </citations>
+    <expand macro="bunwarpj_citations" />
 </tool>
--- a/imagej2_macros.xml	Fri Jun 19 16:59:58 2015 -0400
+++ b/imagej2_macros.xml	Fri Jun 26 05:29:00 2015 -0400
@@ -59,6 +59,10 @@
             </when>
         </conditional>
     </xml>
+    <token name="@max_heap_size_args@">
+        --max_heap_size_type $set_max_heap_size.max_heap_size_type
+        --max_heap_size $set_max_heap_size.max_heap_size
+    </token>
     <xml name="image_datatypes">
         <option value="bmp">bmp</option>
         <option value="gif">gif</option>
@@ -66,12 +70,35 @@
         <option value="png" selected="true">png</option>
         <option value="tiff">tiff</option>
     </xml>
+    <xml name="bunwarpj_citations">
+        <citations>
+            <citation type="bibtex">
+                @InProceedings(Arganda-Carreras2006,
+                    author =     "Ignacio Arganda-Carreras and
+                                        Carlos Oscar S{\'a}nchez Sorzano and
+                                        Roberto Marabini and
+                                        Jos{\'e} Mar\'{\i}a Carazo and
+                                        Carlos Ortiz-de-Solorzano and
+                                        Jan Kybic",
+                    title =          "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",    
+                    publisher =  "Springer Berlin / Heidelberg",    
+                    booktitle =   "Computer Vision Approaches to Medical Image Analysis",
+                    series =       "Lecture Notes in Computer Science",
+                    year =          "2006",
+                    volume =      "4241",
+                    pages =       "85-95",
+                    month =       "May",
+                    city =            "Graz, Austria")
+            </citation>
+            <citation type="doi">10.1038/nmeth.2019</citation>
+        </citations>
+    </xml>
     <xml name="fiji_headless_citations">
         <citations>
             <citation type="doi">10.1038/nmeth.2102</citation>
         </citations>
     </xml>
-    <xml name="citations">
+    <xml name="bioformats_fiji_javabridge_citations">
         <citations>
             <citation type="doi">10.1038/nmeth.2102</citation>
             <citation type="doi">10.1038/nmeth.2019</citation>