Bugfix:

- get rid of hard-coded matlabDCT pathes
- add a check on DCT_DIR and cwd in python scripts

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@784 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Cryst/gtReadSpaceGroup.m

@@ -11,10 +11,15 @@ function [lattice, crystal, table] = gtReadSpaceGroup(sg)
 %       crystal = crystal system for this spacegroup
 %       table   = mhashtable with 'spacegroup' : hermann_mauguin symbol
 %                 
+%     Version 004 20-09-2012 by YGuilhem
+%       Now using GT_MATLAB_HOME to determine path to spacegroups.dat
+%
 %     Version 003 14-05-2012 by LNervo
 %       Add lattice system calculation
 
-fid=fopen( fullfile( getenv('USER'), 'matlabDCT', 'zUtil_Cryst','spacegroups.dat' ),'r');
+global GT_MATLAB_HOME
+
+fid=fopen( fullfile(GT_MATLAB_HOME, 'zUtil_Cryst', 'spacegroups.dat' ),'r');
 C=textscan(fid,'%s %d','delimiter','\t','commentstyle','matlab');
 fclose(fid);
 
@@ -78,4 +83,4 @@ end
 
         
         
-end % end of function
+end % end of function
\ No newline at end of file

zUtil_Help/gtCopyDataForTest.m

@@ -10,7 +10,9 @@ function gtCopyDataForTest(old_pattern,new_pattern,workdir,newdir)
 %       new_pattern = new dataset name
 %       newdir      = new path
 %       workdir     = original path to the dataset directory
-
+%
+%     Version 002 20-09-2012 by YGuilhem
+%       Now using GT_MATLAB_HOME to determine path to tomo_utils.py
 
 if ~exist(fullfile(workdir, old_pattern),'dir')
     disp('Directory doesn''t exist')
@@ -48,24 +50,28 @@ copyfile([ fullfile(workdir, old_pattern, '0_rawdata', 'Orig') '/*'], ...
 
 olddir=pwd;
 
+% Set path to tomo_utils.py script
+global GT_MATLAB_HOME
+tomoUtilsScript = fullfile( GT_MATLAB_HOME, 'zUtil_Python', 'tomo_utils.py');
+
 disp('Renaming the images...')
 cd(fullfile( newdir, new_pattern, '0_rawdata', 'Orig'));
 filenames=[old_pattern '*.edf'];
 if exist([old_pattern '0_0000.edf'],'file')
     image_old=[old_pattern '0_'];
     image_new=[new_pattern '0_'];
-    cmd=['python26 ' fullfile( getenv('HOME'), 'matlabDCT', 'zUtil_Python', 'tomo_utils.py') ...
+    cmd=['python26 ' tomoUtilsScript ...
          ' -rename ''' filenames ''' ''' image_old ''' ''' image_new ''''];
     [s,msg]=unix(cmd);
     disp(msg)
     image_old=[old_pattern '1_'];
     image_new=[new_pattern '1_'];
-    cmd=['python26 ' fullfile( getenv('HOME'), 'matlabDCT', 'zUtil_Python', 'tomo_utils.py') ...
+    cmd=['python26 ' tomoUtilsScript ...
          ' -rename ''' filenames ''' ''' image_old ''' ''' image_new ''''];
     [s,msg]=unix(cmd);
     disp(msg)
 else
-    cmd=['python26 ' fullfile( getenv('HOME'), 'matlabDCT', 'zUtil_Python', 'tomo_utils.py') ...
+    cmd=['python26 ' tomoUtilsScript ...
          ' -rename ''' filenames ''' ''' old_pattern ''' ''' new_pattern ''''];
     [s,msg]=unix(cmd);
     disp(msg)

zUtil_Python/compile_matlab_functions.py

@@ -7,7 +7,7 @@ import sys
 import subprocess
 import string
 
-from xml_dct_io import DCTConf
+from xml_dct_io import DCTConf, DCTCheck
 
 class FunctionsBuilder(object):
 
@@ -79,7 +79,7 @@ class FunctionsBuilder(object):
         print("Generating m-file that will compile those Functions..")
         script_content = [ "function compile(varargin)\n",
                            "current_path = pwd;\n",
-                           "compile_path = [ getenv('HOME') '/matlabDCT/' ];\n",
+                           "compile_path = getenv('DCT_DIR');\n",
                            "cd(compile_path)\n\n",
                            "error_log = java.util.ArrayList();\n\n",
                            "mfiles = java.util.TreeMap();\n" ]
@@ -184,6 +184,7 @@ if __name__=="__main__":
     will_compile = True
     will_generate = True
     force_compile = False
+    DCTCheck().checkCwdWithDCTDir()
     matlab_executable = DCTConf().getMatlabCommand()
     mfiles_to_consider = [ ]
     for index in range(len(sys.argv)):

zUtil_Python/compile_mex_functions.py

@@ -7,7 +7,7 @@ import subprocess
 import string
 import re
 
-from xml_dct_io import DCTConf
+from xml_dct_io import DCTConf, DCTCheck
 
 class MexBuilder(object):
     
@@ -153,7 +153,8 @@ if __name__=="__main__":
                     raise ValueError("Not enough arguments to '-c' option")
         else:
             skip_next = False
-
+    
+    DCTCheck().checkCwdWithDCTDir()
     MexPath = DCTConf().getMexPath()
     builder = MexBuilder(MexPath)
     builder.findMexs()

zUtil_Python/update_DCT_conf.py

@@ -8,14 +8,16 @@ import os
 import datetime
 import shutil
 
+from xml_dct_io import DCTCheck, DCTConf
+
 class ConfUpdater(object):
 
     def __init__(self, base_dir = os.getcwd()):
-        self.base_dir = base_dir;
+        self.base_dir = base_dir
 
     def _getNewFilename(self, filepath):
         timestamp = datetime.datetime.fromtimestamp(os.path.getmtime(filepath))
-        pieces = os.path.splitext(filepath);
+        pieces = os.path.splitext(filepath)
         return (pieces[0] + "-" + timestamp.strftime("%Y-%m-%d-%H-%M") + pieces[1])
 
     def backup(self, filename):
@@ -38,9 +40,17 @@ class ConfUpdater(object):
             print("Creating new file: '%s'" % newfilename)
         self.copy(oldfilename, newfilename)
 
+    def updateXMLConfFile(self):
+        print "Update conf.xml file with current DCT configuration..."
+        conf = DCTConf()
+        conf.setRootDir(os.getenv('DCT_DIR'))
+        conf.save()
+
 if __name__ == '__main__':
     upd = ConfUpdater()
-    confexamplefile = os.path.join("zUtil_Conf", "conf.example.xml")
-    upd.safelyInstallNewFile(confexamplefile, "conf.xml")
-    setupexamplefile = os.path.join("zUtil_Conf", "setup_gt_env.example")
-    upd.safelyInstallNewFile(setupexamplefile, "setup_gt_env")
+    DCTCheck().checkCwdWithDCTDir()
+    #confexamplefile = os.path.join("zUtil_Conf", "conf.example.xml")
+    #upd.safelyInstallNewFile(confexamplefile, "conf.xml")
+    upd.updateXMLConfFile()
+    #setupexamplefile = os.path.join("zUtil_Conf", "setup_gt_env.example")
+    #upd.safelyInstallNewFile(setupexamplefile, "setup_gt_env")

zUtil_Python/xml_dct_io.py

@@ -4,6 +4,8 @@ Created on Dec 27, 2011
 @author: vigano
 '''
 
+import os
+
 try:
     import lxml.etree as ET
 except ImportError as ex:
@@ -25,6 +27,21 @@ class DCTXMLBase(object):
             self.xmlFile = newName
         self.tree.write(self.xmlFile)
 
+class DCTCheck(object):
+
+    def checkCwdWithDCTDir(self, dctdir = os.getenv('DCT_DIR')):
+        print "Checking if current directory matches with DCT_DIR environment variable...",
+        indir = os.getcwd()
+        try:
+            os.chdir(dctdir)
+            testdir = os.getcwd()
+        except:
+            raise EnvironmentError("DCT_DIR environment variable (%s) points to inexistent directory!" % dctdir)
+        os.chdir(indir)
+        if indir == testdir:
+            print "OK"
+        else:
+            raise EnvironmentError("Current working directory does not match with DCT_DIR environment variable!\n%s != %s" % (indir, dctdir))
 
 class DCTConf(DCTXMLBase):