Merge branch 'release-1.12'

.gitignore

@@ -1,5 +1,5 @@
 *~
 *\#
 \.\#*
-\.swp
+*\.swp
 *\.pyc

NEWS

@@ -1,3 +1,25 @@
+New in Version 1.12
+===================
+* LSQ6 (MBM) fixes to the combination of --no-nuc and --inormalize. This would incorrectly apply the lsq6 transformation to the inormalized file twice
+* MAGeT -- now uses the pipeline_name argument -- has better error messages when there are issues with the atlases/labels/masks -- if no atlases are found in the atlas library, the program exists -- has an explicit way to specify --pairwise
+* improvements to error handling in the code
+* most pipeline related files and directories are now prefixed with the pipeline name
+* fixes to how the initial model is used. Now there are two possible scenarios:
+
+  image.mnc
+  image_mask.mnc
+
+  or
+
+  image.mnc
+  image_mask.mnc
+  image_native.mnc
+  image_native_mask.mnc
+  image_native_to_standard.xfm
+
+* debug statements added in order to inspect heartbeat issues -- heartbeat checking can also be turned off at the moment
+* on SciNet, as many executors as possible will start with the server using syncwith rather than after (in qsub)
+
 New in Version 1.11
 ===================
 (in addition to the changes in the alpha version)

applications/MAGeT.py

@@ -50,7 +50,13 @@ def run(self):
             print "You can find the default MAGeT protocols in your pydpiper source directory, in: applications_testing/test_data/"
             sys.exit()
 
-
+        # There are two variables that can be used to determine where the output
+        # of the pipeline is stored: pipeline_name and outputDir
+        # If the outputDir is not specified, the current working directory is used.
+        if self.options.pipeline_name:
+            self.outputDir += "/" + self.options.pipeline_name
+            fh.makedirsIgnoreExisting(self.outputDir)
+
         atlasDir = fh.createSubDir(self.outputDir, "input_atlases")
 
         """Read in atlases from directory specified in --atlas-library and 
@@ -72,14 +78,13 @@ def run(self):
             else:
                 average.append(abspath(inFile))
         # check to make sure len(average)==len(labels)
-        if not len(average) == len(labels):
-            logger.error("Number of input atlas labels does not match averages.")
-            logger.error("Check " + str(self.options.atlas_lib) + " and try again.")
+        if (not len(average) == len(labels)) or (not len(average) == len(masks)):
+            print "\nError: not all atlases/labels/masks match."
+            print "The allowed naming conventions are:\n{atlas}.mnc\n{atlas}_labels.mnc\n{atlas}_mask.mnc"
+            print "\nand:\n{atlas}_average.mnc\n{atlas}_labels.mnc\n{atlas}_mask.mnc\n"
+            print "Check the atlas library directory: " + str(self.options.atlas_lib) + " and try again."
+            print "Exiting..."
             sys.exit() 
-        elif not len(average) == len(masks):
-            logger.error("Number of input atlas masks does not match averages.")
-            logger.error("Check " + str(self.options.atlas_lib) + " and try again.")
-            sys.exit()
         else:
         # match labels with averages
             numLibraryAtlases = len(labels)
@@ -98,7 +103,13 @@ def run(self):
                         break
                 atlasPipeFH.addLabels(abspath(iLabel), inputLabel=True) 
                 atlases.append(atlasPipeFH)
-
+
+        # exit if no atlases were found in the specified directory
+        if numLibraryAtlases == 0:
+            print "\nError: no atlases were found in the specified directory: %s" % self.options.atlas_lib
+            print "Exiting..."
+            sys.exit()
+
         #MF TODO: add some checking to make sure that atlas/labels/naming all worked correctly
         # eg if we have A4_mask.mnc "matching" with A3_labels, we wont get right thing.
 

atoms_and_modules/LSQ6.py

@@ -57,7 +57,9 @@ def addLSQ6ArgumentGroup(parser):
     group.add_argument("--lsq6-simple", dest="lsq6_method",
                      action="store_const", const="lsq6_simple",
                      help="Run a 6 parameter alignment assuming that the input files are roughly "
-                     "aligned: same space, similar orientation. [Default = %(default)s]")
+                     "aligned: same space, similar orientation. Keep in mind that if you use an "
+                     "initial model with both a standard and a native space, the assumption is "
+                     "that the input files are already roughly aligned to the native space [Default = %(default)s]")
     group.add_argument("--lsq6-centre-estimation", dest="lsq6_method",
                      action="store_const", const="lsq6_centre_estimation",
                      help="Run a 6 parameter alignment assuming that the input files have a "
@@ -313,9 +315,16 @@ def setupPipeline(self):
             self.p.addPipeline(nucorrection.p)
 
         if self.options.inormalize:
+            need_to_resample_to_LSQ6 = True;
+            # Currently when no non-uniformity correction is applied, the input 
+            # file is intensity normalized in lsq6 space, not native space. This 
+            # means that in that case, we do not need to resample to LSQ6 anymore
+            # since the file is already in that space:
+            if not self.options.nuc:
+                need_to_resample_to_LSQ6 = False
             intensity_normalization = IntensityNormalization(self.inputFiles,
                                                              initial_model=self.initModel,
-                                                             resampleINORMtoLSQ6=True,
+                                                             resampleINORMtoLSQ6=need_to_resample_to_LSQ6,
                                                              targetForLSQ6=self.target)
             self.p.addPipeline(intensity_normalization.p)
 

atoms_and_modules/MAGeT_modules.py

@@ -14,9 +14,13 @@ def addMAGeTArgumentGroup(parser):
     group.add_argument("--atlas-library", dest="atlas_lib",
                        type=str, default="atlas_label_pairs",
                        help="Directory of existing atlas/label pairs")
+    group.add_argument("--pairwise", dest="pairwise",
+                       action="store_true",
+                       help="""If specified, register inputs to each other pairwise. [Default]""")
     group.add_argument("--no-pairwise", dest="pairwise",
-                       action="store_false", default=True,
-                       help="""Pairwise crossing of templates. [Default = %(default)s]. If specified, only register inputs to atlases in library""")
+                       action="store_false",
+                       help="""If specified, only register inputs to atlases in library.""")
+    parser.set_defaults(pairwise=True)
     group.add_argument("--mask", dest="mask",
                        action="store_true", default=False,
                        help="Create a mask for all images prior to handling labels. [Default = %(default)s]")

atoms_and_modules/minc_atoms.py

@@ -74,8 +74,8 @@ def __init__(self,
                 if self.useMask:
                     self.target_mask = target_mask
         except:
-            print "Failed in putting together mincANTS command."
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together mincANTS command; unexpected error: "
+            raise
 
         self.similarity_metric = similarity_metric
         self.weight = weight 
@@ -218,8 +218,8 @@ def __init__(self,
                     self.source_mask = source_mask
                     self.target_mask = target_mask 
         except:
-            print "Failed in putting together minctracc command."
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together minctracc command; unexpected error: "
+            raise
 
         self.linearparam = linearparam       
         self.iterations = str(iterations)
@@ -354,8 +354,8 @@ def __init__(self,
                     gradientBase = blurBase.replace("blur", "dxyz")
                     self.outputFiles += ["".join([gradientBase, ".mnc"])] 
         except:
-            print "Failed in putting together blur command."
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together blur command; unexpected error: "
+            raise
 
         self.cmd = ["mincblur", "-clobber", "-no_apodize", "-fwhm", str(fwhm),
                     self.inputFiles[0], self.base]
@@ -371,8 +371,7 @@ def __init__(self,
         # characters. Given that we don't know which version of mincblur is installed 
         # (this should and will be fixed at some point in the future), we'll exit here
         if len(self.outputFiles[0]) > 264:
-            print "\n\nError: mincblur (potentially) has a hardcoded limit for the allowed length of the output file. The following command will not be able to run: \n\n%s\n\nPlease rename your input files/paths to make sure the filenames become shorter.\n" % self.cmd
-            sys.exit()
+            raise Exception("mincblur (potentially) has a hardcoded limit for the allowed length of the output file. The following command will not be able to run: \n\n%s\n\nPlease rename your input files/paths to make sure the filenames become shorter.\n" % self.cmd)
 
 class autocrop(CmdStage):
     def __init__(self, 
@@ -407,7 +406,7 @@ def __init__(self,
 
         except:
             print "Failed in putting together autocrop command"
-            print "Unexpected error: ", sys.exc_info()
+            raise
 
         self.addDefaults()
         self.finalizeCommand()
@@ -528,11 +527,8 @@ def __init__(self,
         argarray could contain inFile and/or output files
         """
 
-        argArray = kwargs.pop("argArray", None)
-        if not argArray:
-            CmdStage.__init__(self, ["mincresample"])
-        else:
-            CmdStage.__init__(self, ["mincresample"] + argArray)
+        argArray = kwargs.pop("argArray", [])
+        CmdStage.__init__(self, ["mincresample"] + argArray)
 
         try:
             #MF TODO: What if we don't want to use lastBasevol?  
@@ -592,8 +588,8 @@ def __init__(self,
                     self.logFile = logFile
 
         except:
-            print "Failed in putting together resample command"
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together resample command; unexpected error: "
+            raise
 
         self.addDefaults()
         self.finalizeCommand()
@@ -756,8 +752,8 @@ def __init__(self,
                     self.logFile = logFile
 
         except:
-            print "Failed in putting together mincaverage command"
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together mincaverage command; unexpected error: "
+            raise
 
         self.addDefaults()
         self.finalizeCommand()
@@ -864,8 +860,7 @@ def __init__(self,
                 self.source = inSource
                 self.target = inTarget
         except:
-            print "Failed in putting together RotationalMinctracc command."
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together RotationalMinctracc command; unexpected error:"
             raise
 
         # The resolution is used to determine the step size and 
@@ -929,8 +924,7 @@ def finalizeCommand(self,
                     self.cmd += ["-m", mask]
                     self.inputFiles.append(mask)
             except:
-                print "Failed retrieving information about a mask for the target in RotationalMinctracc."
-                print "Unexpected error: ", sys.exc_info()
+                print "Failed retrieving information about a mask for the target in RotationalMinctracc; unexpected error: "
                 raise
 
 
@@ -998,8 +992,8 @@ def __init__(self,
                     self.logFile = logFile
 
         except:
-            print "Failed in putting together xfminvert command"
-            print "Unexpected error: ", sys.exc_info()
+            print "Failed in putting together xfminvert command; unexpected error: "
+            raise
 
         self.finalizeCommand()
         self.setName()