Merge branch 'release-1.7'

INSTALL

@@ -8,11 +8,11 @@ Run: python setup.py install
 
 Dependencies: 
 
-Pyro - http://irmen.home.xs4all.nl/pyro/
+Pyro4 - http://pythonhosted.org/Pyro4
 NetworkX - http://networkx.lanl.gov/
 Py.test - http://pytest.org/
 
-In Ubuntu (tested on 10.04), run: 
+In Ubuntu (tested on 12.04), run: 
 	apt-get install python-networkx
 	pip install pyro
-	pip install pytest
+	pip install pytest

NEWS

@@ -1,3 +1,20 @@
+New in Version 1.7
+==================
+* the communication between the server and the executors has been upgraded
+  from Pyro3 to Pyro4. Currently the following environment variables should
+  be set:
+
+  PYRO_DETAILED_TRACEBACK=True
+  PYRO_COMMTIMEOUT=2
+  PYRO_SERVERTYPE=multiplex
+  PYRO_LOGLEVEL=DEBUG
+
+* the stiffness, weight and similarity parameters for minctracc can now be
+  set through the non linear protocol in MBM.py 
+* all output from the server/executors will be stored in the current 
+  working directory
+
+
 New in Version 1.6
 ====================
 * fix to MAGeT.py. Solves issues with the voxel_vote command. 

applications/#MBM.py#

@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+
+from pydpiper.application import AbstractApplication
+import atoms_and_modules.registration_functions as rf
+import atoms_and_modules.registration_file_handling as rfh
+import atoms_and_modules.LSQ6 as lsq6
+import atoms_and_modules.LSQ12 as lsq12
+import atoms_and_modules.NLIN as nlin
+import atoms_and_modules.minc_parameters as mp
+import atoms_and_modules.stats_tools as st
+import Pyro
+import os
+from optparse import OptionGroup
+import logging
+
+
+logger = logging.getLogger(__name__)
+
+Pyro.config.PYRO_MOBILE_CODE=1 
+
+def addMBMGroup(parser):
+    group = OptionGroup(parser, "MBM options", 
+                        "Options for MICe-build-model.")
+    parser.add_option_group(group)
+
+class MBMApplication(AbstractApplication):
+    def setup_options(self):
+        """Add option groups from specific modules"""
+        addMBMGroup(self.parser)
+        rf.addGenRegOptionGroup(self.parser)
+        lsq6.addLSQ6OptionGroup(self.parser)
+        lsq12.addLSQ12OptionGroup(self.parser)
+        nlin.addNlinRegOptionGroup(self.parser)
+        st.addStatsOptions(self.parser)
+
+        self.parser.set_usage("%prog [options] input files") 
+
+    def setup_appName(self):
+        appName = "MICe-build-model"
+        return appName
+
+    def run(self):
+        options = self.options
+        args = self.args
+
+        # Setup output directories for different registration modules.        
+        dirs = rf.setupDirectories(self.outputDir, options.pipeline_name, module="ALL")
+        inputFiles = rf.initializeInputFiles(args, dirs.processedDir, maskDir=options.mask_dir)
+
+        #Setup init model and inital target. Function also exists if no target was specified.
+        initModel, targetPipeFH = rf.setInitialTarget(options.init_model, 
+                                                      options.lsq6_target, 
+                                                      dirs.lsq6Dir,
+                                                      self.outputDir)
+
+        #LSQ6 MODULE, NUC and INORM
+        runLSQ6NucInorm = lsq6.LSQ6NUCInorm(inputFiles,
+                                            targetPipeFH,
+                                            initModel, 
+                                            dirs.lsq6Dir, 
+                                            options)
+        self.pipeline.addPipeline(runLSQ6NucInorm.p)
+
+        # LSQ12 MODULE
+        # We need to specify a likeFile/space when all files are resampled
+        # at the end of LSQ12. If one is not specified, use standard space. 
+        if options.lsq12_likeFile == None:
+            targetPipeFH = initModel[0]
+        else:
+            targetPipeFH = rfh.RegistrationFHBase(os.path.abspath(options.lsq12_likeFile), 
+                                                  basedir=dirs.lsq12Dir)
+        lsq12module = lsq12.FullLSQ12(inputFiles, 
+                                      dirs.lsq12Dir, 
+                                      likeFile=targetPipeFH, 
+                                      maxPairs=None, 
+                                      lsq12_protocol=options.lsq12_protocol,
+                                      subject_matter=options.lsq12_subject_matter)
+        lsq12module.iterate()
+        self.pipeline.addPipeline(lsq12module.p)
+
+        #TODO: Additional NUC step here. This will impact both the lsq6 and lsq12 modules. 
+        # May want to not do resampling and averaging by default. TBD. 
+
+        #Target mask for registration--I HATE this hack, as is noted in check-in and
+        #as a github issue. 
+        if lsq12module.lsq12AvgFH.getMask()== None:
+            if initModel[0]:
+                lsq12module.lsq12AvgFH.setMask(initModel[0].getMask())
+
+        #NLIN MODULE - Register with minctracc or mincANTS based on options.reg_method
+        nlinObj = nlin.initializeAndRunNLIN(dirs.lsq12Dir,
+                                            inputFiles,
+                                            dirs.nlinDir,
+                                            avgPrefix=options.pipeline_name,
+                                            createAvg=False,
+                                            targetAvg=lsq12module.lsq12AvgFH,
+                                            nlin_protocol=options.nlin_protocol,
+                                            reg_method=options.reg_method)
+
+        self.pipeline.addPipeline(nlinObj.p)
+        self.nlinAverages = nlinObj.nlinAverages
+
+        #STATS MODULE
+        if options.calc_stats:
+            #Choose final average from array of nlin averages
+            finalNlin = self.nlinAverages[-1]
+            # For each input file, calculate statistics from final average (finalNlin) 
+            # to the inputFH space where all linear differences have been accounted for (LSQ12). 
+            # The additionalXfm specified for each inputFH is the transform from the lsq6 to lsq12 
+            # space for that scan. This encapsulates linear differences and is necessary for
+            # some of the calculations in CalcStats.  
+            for inputFH in inputFiles:
+                stats = st.CalcStats(inputFH, 
+                                     finalNlin, 
+                                     options.stats_kernels,
+                                     additionalXfm=lsq12module.lsq12AvgXfms[inputFH])
+                self.pipeline.addPipeline(stats.p)
+
+if __name__ == "__main__":
+
+    application = MBMApplication()
+    application.start()
+

applications/MAGeT.py

@@ -7,7 +7,6 @@
 from atoms_and_modules.MAGeT_modules import MAGeTMask, MAGeTRegister, voxelVote, addMAGeTOptionGroup
 from atoms_and_modules.LSQ12 import addLSQ12OptionGroup
 from atoms_and_modules.NLIN import addNlinRegOptionGroup
-import Pyro
 from os.path import abspath, join
 import logging
 import glob
@@ -16,8 +15,6 @@
 
 logger = logging.getLogger(__name__)
 
-Pyro.config.PYRO_MOBILE_CODE=1 
-
 class MAGeTApplication(AbstractApplication):
     def setup_options(self):
         addGenRegOptionGroup(self.parser)

applications/MBM.py

@@ -8,16 +8,13 @@
 import atoms_and_modules.NLIN as nlin
 import atoms_and_modules.minc_parameters as mp
 import atoms_and_modules.stats_tools as st
-import Pyro
 import os
 from optparse import OptionGroup
 import logging
 
 
 logger = logging.getLogger(__name__)
 
-Pyro.config.PYRO_MOBILE_CODE=1 
-
 def addMBMGroup(parser):
     group = OptionGroup(parser, "MBM options", 
                         "Options for MICe-build-model.")
@@ -120,4 +117,4 @@ def run(self):
 
     application = MBMApplication()
     application.start()
-
+

applications/pairwise_nlin.py

@@ -8,7 +8,6 @@
 import atoms_and_modules.minc_atoms as ma
 import atoms_and_modules.stats_tools as st
 import atoms_and_modules.option_groups as og
-import Pyro
 from optparse import OptionGroup
 from datetime import date
 from os.path import abspath, isdir
@@ -17,8 +16,6 @@
 
 logger = logging.getLogger(__name__)
 
-Pyro.config.PYRO_MOBILE_CODE=1 
-
 """NOTE: This application needs a significant overhaul and/or combining with the RegistrationChain
          Application. Until this comment is removed, please consider this class DEPRECATED."""
 

applications/registration_chain.py

@@ -11,16 +11,13 @@
 import atoms_and_modules.NLIN as nlin
 import atoms_and_modules.stats_tools as st
 import atoms_and_modules.minc_parameters as mp
-import Pyro
 from optparse import OptionGroup
 from os.path import abspath, isdir, isfile
 import logging
 import sys
 
 logger = logging.getLogger(__name__)
 
-Pyro.config.PYRO_MOBILE_CODE=1 
-
 def addRegChainOptionGroup(parser):
     """option group for the command line argument parser"""
     group = OptionGroup(parser, "Registration-chain options", 

applications/twolevel_model_building.py

@@ -9,15 +9,12 @@
 import atoms_and_modules.NLIN as nl
 import atoms_and_modules.stats_tools as st
 import atoms_and_modules.registration_file_handling as rfh
-import Pyro
 from os.path import split, splitext, abspath
 import sys
 import logging
 
 logger = logging.getLogger(__name__)
 
-Pyro.config.PYRO_MOBILE_CODE=1 
-
 class LongitudinalTwolevelNlin(AbstractApplication):
     def setup_options(self):
         helpString="""

applications_testing/test_data/minctracc_example_nlin_protocol.csv

@@ -5,3 +5,6 @@
 "gradient";TRUE;TRUE;TRUE;TRUE;TRUE;TRUE
 "w_translations";0.4;0.4;0.4;0.4;0.4;0.4
 "optimization";"-use_simplex";"-use_simplex";"-use_simplex";"-use_simplex";"-use_simplex";"-use_simplex"
+"stiffness";0.5;0.5;0.5;0.5;0.5;0.5
+"weight";0.3;0.3;0.3;0.3;0.3;0.3
+"similarity";0.5;0.5;0.5;0.5;0.5;0.5