Merge pull request #159 from martinschorb/patch-2

pass `resolutionUnit` parameter

Author: RussTorres

LICENSE

@@ -1,33 +1,25 @@
-Allen Institute Software License – This software license is the 2-clause BSD 
-license plus a third clause that prohibits redistribution and use for 
-commercial purposes without further permission. 
+BSD 2-Clause License
 
-Copyright © 2019. Allen Institute.  All rights reserved.
+Copyright (c) 2022, Allen Institute
+All rights reserved.
 
-Redistribution and use in source and binary forms, with or without 
+Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-1. Redistributions of source code must retain the above copyright notice, this 
-list of conditions and the following disclaimer.
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
 
-2. Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
-and/or other materials provided with the distribution.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
 
-3. Redistributions and use for commercial purposes are not permitted without 
-the Allen Institute’s written permission. For purposes of this license, 
-commercial purposes are the incorporation of the Allen Institute's software 
-into anything for which you will charge fees or other compensation or use of 
-the software to perform a commercial service for a third party. Contact 
-[email protected] for commercial licensing opportunities.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -32,4 +32,8 @@ Documentation
 #############
 http://render-python.readthedocs.io/en/latest/
 
+Government Sponsorship
+######################
+Supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Interior / Interior Business Center (DoI/IBC) contract number D16PC00004. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation thereon. Disclaimer: The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of IARPA, DoI/IBC, or the U.S. Government.
+
 .. _render :

renderapi/client/client_calls.py

@@ -415,10 +415,11 @@ def renderSectionClient(stack, rootDirectory, zs, scale=None,
                         maxIntensity=None, minIntensity=None, bounds=None,
                         format=None, channel=None, customOutputFolder=None,
                         customSubFolder=None, padFileNamesWithZeros=None,
-                        doFilter=None, fillWithNoise=None, imageType=None,
-                        subprocess_mode=None, host=None, port=None, owner=None,
-                        project=None, client_script=None, memGB=None,
-                        render=None, **kwargs):
+                        resolutionUnit=None, doFilter=None, fillWithNoise=None,
+                        imageType=None, subprocess_mode=None, host=None,
+                        port=None, owner=None, project=None,
+                        client_script=None, memGB=None, render=None,
+                        **kwargs):
     """run RenderSectionClient.java
 
     Parameters
@@ -448,6 +449,9 @@ def renderSectionClient(stack, rootDirectory, zs, scale=None,
         folder to save all images in under outputFolder (overrides default of none)
     padFileNamesWithZeros: bool
         whether to pad file names with zeros to make sortable
+    resolutionUnit: str
+        if format is tiff and unit is specified (e.g. as 'nm'), include resolution data 
+        in rendered tiff headers.
     imageType: int
         8,16,24 to specify what kind of image type to save
     doFilter : str
@@ -487,9 +491,11 @@ def renderSectionClient(stack, rootDirectory, zs, scale=None,
              get_param(customOutputFolder, '--customOutputFolder') +
              get_param(imageType, '--imageType') +
              get_param(channel, '--channels') +
-             get_param(customSubFolder, '--customSubFolder') +
+             get_param(customSubFolder, '--customSubFolder') +             
              get_param(padFileNamesWithZeros, '--padFileNamesWithZeros') +
+             get_param(resolutionUnit, '--resolutionUnit') +
              bound_param + zs)
+    
     call_run_ws_client('org.janelia.render.client.RenderSectionClient',
                        memGB=memGB, client_script=client_script,
                        subprocess_mode=subprocess_mode, add_args=argvs,