def OnBake(self, event=None):
out_dir = self.dcOutput.GetPath()
if self.cbSpawnWorkerProcs.GetValue():
num_procs = batchProcess.NUM_PROCS
else:
num_procs = 1
#validate our choices:
if (self.rm.activeRecipe is None) or (len(self.rm.activeRecipe.modules) == 0):
wx.MessageBox('No Recipe: Please open (or build) a recipe', 'Error', wx.OK|wx.ICON_ERROR)
return
inputs = [l.filenames for l in self._file_lists]
if not len(inputs[0]) > 0:
wx.MessageBox('No input files', 'Error', wx.OK|wx.ICON_ERROR)
return
if (out_dir == '') or not os.path.exists(out_dir):
wx.MessageBox('Ouput directory does not exist', 'Error', wx.OK|wx.ICON_ERROR)
return
#old_style_output = any([('output' in m.outputs) for m in self.rm.activeRecipe.modules])
if not any([isinstance(m, modules.base.OutputModule) for m in self.rm.activeRecipe.modules]):
# no output module defined
# if old_style_output:
# #old style output, warn and give option to continue
# if not wx.MessageBox(
# "Relying on old-style magic 'output' variable, consider using output modules instead. Continue?",
# 'Warning', wx.OK|wx.CANCEL|wx.ICON_WARNING) == wx.OK:
# return
# else:
wx.MessageBox('No outputs defined - add an output module', 'Error', wx.OK | wx.ICON_ERROR)
return
# elif old_style_output:
# wx.MessageBox("Both new and old style outputs defined, choose another name for the 'output' variable", 'Error', wx.OK | wx.ICON_ERROR)
# return
if (len(inputs[1]) > 0) and not (len(inputs[0]) == len(inputs[1])):
wx.MessageBox('Length of input file lists not equal', 'Error', wx.OK | wx.ICON_ERROR)
return
from PYME.ui import progress
try:
with progress.ComputationInProgress(self, 'Batch Analysis'):
if not len(inputs[1]) > 0:
batchProcess.bake(self.rm.activeRecipe, {'input':inputs[0]}, out_dir, num_procs=num_procs, metadata_defaults=self._default_md)
else:
batchProcess.bake(self.rm.activeRecipe, {'input':inputs[0], 'input2':inputs[1]}, out_dir, num_procs=num_procs, metadata_defaults=self._default_md)
except:
if (num_procs > 1):
wx.MessageBox('Uncheck "spawn worker process for each core" for easier debugging', 'Error occurred during multiple process run', wx.OK | wx.ICON_ERROR)
raise
def OnBake(self, event=None):
out_dir = self.dcOutput.GetPath()
if self.cbSpawnWorkerProcs.GetValue():
num_procs = batchProcess.NUM_PROCS
else:
num_procs = 1
#validate our choices:
if (self.rm.activeRecipe is None) or (len(self.rm.activeRecipe.modules)
== 0):
wx.MessageBox('No Recipe: Please open (or build) a recipe',
'Error', wx.OK | wx.ICON_ERROR)
return
if not len(self.inputFiles) > 0:
wx.MessageBox('No input files', 'Error', wx.OK | wx.ICON_ERROR)
return
if (out_dir == '') or not os.path.exists(out_dir):
wx.MessageBox('Ouput directory does not exist', 'Error',
wx.OK | wx.ICON_ERROR)
return
if not len(self.inputFiles) == len(self.inputFiles2):
batchProcess.bake(self.rm.activeRecipe, {'input': self.inputFiles},
out_dir,
num_procs=num_procs)
else:
batchProcess.bake(self.rm.activeRecipe, {
'input': self.inputFiles,
'input2': self.inputFiles2
},
out_dir,
num_procs=num_procs)
def on_bake(image, parentWindow=None, glCanvas=None):
with wx.FileDialog(parentWindow, "Choose all series", wildcard='H5 (*.h5)|*.h5',
style=wx.FD_OPEN | wx.FD_MULTIPLE) as dialog:
if dialog.ShowModal() == wx.ID_CANCEL:
return
filelist = dialog.GetPaths()
inputGlobs = {'input' : filelist}
map_dir = os.path.dirname(filelist[0])
output_dir = os.path.join(map_dir,'analysis')
if not os.path.exists(output_dir):
os.makedirs(output_dir)
recipe_str = """
- processing.DarkAndVarianceMap:
input: input
output_dark: dark
output_variance: variance
- output.ImageOutput:
filePattern: '{output_dir}/{file_stub}_dark.tif'
inputName: dark
- output.ImageOutput:
filePattern: '{output_dir}/{file_stub}_variance.tif'
inputName: variance
"""
recipe = modules.ModuleCollection.fromYAML(recipe_str)
bake(recipe, inputGlobs, output_dir)