first commit

base.py

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+'''Base objects and functionality.'''
+
+import sys
+import shutil
+import os
+import time
+import glob
+
+class ProcessingObject():
+	"""Base object with the properties shared by all processing
+	objects."""
+	overwrite = False
+	waitfornext = True
+	verbose = True
+	channelout = sys.stdout.writelines
+	update = False
+	parallel = False
+	inext = '.nii'
+	outext = '.nii'
+
+	def findStrInList(self,searchstr,targetlist):
+		'''Use a list comp search method to find a target string in each of
+		the strings in targetlist. Numerous assumptions: 1) error if no
+		matches, 2) only one match should be found.'''
+		hits = [x for x in targetlist if searchstr in x]
+		if not hits: 
+			raise Exception('No matches for %s' % searchstr)
+		return hits
+
+	def findListItemInStr(self,searchstr,targetlist):
+		'''Use a list comp search method to find a target string in each of
+		the strings in targetlist. Numerous assumptions: 1) error if no
+		matches, 2) only one match should be found.'''
+		hits = [x for x in targetlist if x in searchstr]
+		if not hits: 
+			raise Exception('No matches for %s' % searchstr)
+		return hits
+
+	def output(self,text):
+		'''Write out text to e.g. stdout but only if verbose.'''
+		if type(text) is not list:
+			text = [text]
+		if self.verbose:
+			self.channelout(('%s\n' % s for s in text))
+		return
+
+	def checkInputs(self,argdict):
+		for attribute in argdict:
+			if hasattr(self,attribute):
+				#self.output('Updating attribute: %s' % attribute)
+				setattr(self,attribute,argdict[attribute])
+			else:
+				raise Exception('Unknown argument: %s' % attribute)
+		return
+
+	def getOutput(self,invol,sd):
+		"""The default getOutput method converts an invol to an outvol
+		based on various object settings. Inherited objects can overwrite
+		with methods based on checking attributes internally instead."""
+		outpath,outfile = os.path.split(invol[0])
+		outfn,outext = os.path.splitext(outfile)
+		return self.addPrefix(os.path.join(outpath,outfn + self.outext)
+				,self.outprefix)
+
+	def checkOutput(self,outvol):
+		"""Use the output from getOutput to decide if the task has already
+		been done (ie, there is output) or not. To be overwritten with
+		getOutput by processes that don't use volumes as output."""
+		# Support wild card matching for the adventurous
+		if '*' in outvol:
+			return len(glob.glob(outvol)) >= 1
+		else:
+			return os.path.exists(outvol)
+
+	def setAllInputs(self,argdict):
+		for attribute in argdict:
+			setattr(self,attribute,argdict[attribute])
+		return
+
+	def mkAnaDir(self,anadir):
+		'''Make a directory while remaining conscious of existing dirs and
+		overwrite settings.'''
+		# Check if we need to worry about overwriting
+		if os.path.exists(anadir):
+			if self.overwrite:
+				self.output('Creating %s after removing old dir' % anadir)
+				shutil.rmtree(anadir)
+			elif self.update:
+				self.output('%s already exists, continuing' % anadir)
+				return False
+			else:
+				raise Exception('%s already exists!' % anadir)
+		os.mkdir(anadir)
+		return True
+
+	def initialiseLog(self,logfile):
+		"""Make a log file that stdout gets piped to."""
+		timestr = time.strftime('%y%m%d_%H%M')
+		if os.path.exists(logfile) and not self.overwrite:
+			F = open(logfile,'a')
+		else:
+			F = open(logfile,'w')
+		F.write('\n\nbatchbrain on %s...\n' % timestr)
+		F.close()
+		return
+
+