def image_directory(self):
"""Return the image directory
"""
if self.location == DIR_DEFAULT_IMAGE:
return preferences.get_default_image_directory()
elif self.location == DIR_DEFAULT_OUTPUT:
return preferences.get_default_output_directory()
else:
return preferences.get_absolute_path(self.location_other.value)
def image_directory(self):
"""Return the image directory
"""
if self.location == DIR_DEFAULT_IMAGE:
return preferences.get_default_image_directory()
elif self.location == DIR_DEFAULT_OUTPUT:
return preferences.get_default_output_directory()
else:
return preferences.get_absolute_path(self.location_other.value)
def save_pipeline(self, workspace, outf=None):
'''Save the pipeline in Batch_data.mat
Save the pickled image_set_list state in a setting and put this
module in batch mode.
if outf is not None, it is used as a file object destination.
'''
from cellprofiler.utilities.get_revision import version
if self.wants_default_output_directory.value:
path = cpprefs.get_default_output_directory()
else:
path = cpprefs.get_absolute_path(self.custom_output_directory.value)
h5_path = os.path.join(path, F_BATCH_DATA_H5)
image_set_list = workspace.image_set_list
pipeline = workspace.pipeline
m = cpmeas.Measurements(copy = workspace.measurements,
filename = h5_path)
assert isinstance(image_set_list, cpi.ImageSetList)
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(m, cpmeas.Measurements)
pipeline = pipeline.copy()
target_workspace = cpw.Workspace(pipeline, None, None, None,
m, image_set_list,
workspace.frame)
pipeline.prepare_to_create_batch(target_workspace, self.alter_path)
bizarro_self = pipeline.module(self.module_num)
assert isinstance(bizarro_self, CreateBatchFiles)
state = image_set_list.save_state()
state = zlib.compress(state)
bizarro_self.revision.value = version
bizarro_self.batch_state = np.array(state)
if self.wants_default_output_directory:
bizarro_self.custom_output_directory.value = \
self.alter_path(cpprefs.get_default_output_directory())
bizarro_self.default_image_directory.value = \
self.alter_path(cpprefs.get_default_image_directory())
bizarro_self.batch_mode.value = True
pipeline.write_pipeline_measurement(m)
if outf is None:
mat_path = os.path.join(path, F_BATCH_DATA)
if os.path.exists(mat_path) and workspace.frame is not None:
import wx
if (wx.MessageBox("%s already exists. Do you want to overwrite it?"%
mat_path,
"Overwriting %s" % F_BATCH_DATA,
wx.YES_NO, workspace.frame) == wx.NO):
return
pipeline.save(mat_path, format=cpp.FMT_MATLAB) # Matlab... it's like the vestigial hole in the head of CP.
else:
pipeline.save(outf, format=cpp.FMT_NATIVE)
def save_pipeline(self, workspace, outf=None):
'''Save the pipeline in Batch_data.mat
Save the pickled image_set_list state in a setting and put this
module in batch mode.
if outf is not None, it is used as a file object destination.
'''
from cellprofiler.utilities.version import version_number
if outf is None:
if self.wants_default_output_directory.value:
path = cpprefs.get_default_output_directory()
else:
path = cpprefs.get_absolute_path(self.custom_output_directory.value)
h5_path = os.path.join(path, F_BATCH_DATA_H5)
else:
h5_path = outf
image_set_list = workspace.image_set_list
pipeline = workspace.pipeline
m = cpmeas.Measurements(copy = workspace.measurements,
filename = h5_path)
try:
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(m, cpmeas.Measurements)
orig_pipeline = pipeline
pipeline = pipeline.copy()
# this use of workspace.frame is okay, since we're called from
# prepare_run which happens in the main wx thread.
target_workspace = cpw.Workspace(pipeline, None, None, None,
m, image_set_list,
workspace.frame)
pipeline.prepare_to_create_batch(target_workspace, self.alter_path)
bizarro_self = pipeline.module(self.module_num)
bizarro_self.revision.value = version_number
if self.wants_default_output_directory:
bizarro_self.custom_output_directory.value = \
self.alter_path(cpprefs.get_default_output_directory())
bizarro_self.default_image_directory.value = \
self.alter_path(cpprefs.get_default_image_directory())
bizarro_self.batch_mode.value = True
pipeline.write_pipeline_measurement(m)
orig_pipeline.write_pipeline_measurement(m, user_pipeline=True)
#
# Write the path mappings to the batch measurements
#
m.write_path_mappings(
[(mapping.local_directory.value, mapping.remote_directory.value)
for mapping in self.mappings])
return h5_path
finally:
m.close()
def save_pipeline(self, workspace, outf=None):
'''Save the pipeline in Batch_data.mat
Save the pickled image_set_list state in a setting and put this
module in batch mode.
if outf is not None, it is used as a file object destination.
'''
from cellprofiler.utilities.version import version_number
if outf is None:
if self.wants_default_output_directory.value:
path = cpprefs.get_default_output_directory()
else:
path = cpprefs.get_absolute_path(self.custom_output_directory.value)
h5_path = os.path.join(path, F_BATCH_DATA_H5)
else:
h5_path = outf
image_set_list = workspace.image_set_list
pipeline = workspace.pipeline
m = cpmeas.Measurements(copy=workspace.measurements,
filename=h5_path)
try:
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(m, cpmeas.Measurements)
orig_pipeline = pipeline
pipeline = pipeline.copy()
# this use of workspace.frame is okay, since we're called from
# prepare_run which happens in the main wx thread.
target_workspace = cpw.Workspace(pipeline, None, None, None,
m, image_set_list,
workspace.frame)
pipeline.prepare_to_create_batch(target_workspace, self.alter_path)
bizarro_self = pipeline.module(self.module_num)
bizarro_self.revision.value = version_number
if self.wants_default_output_directory:
bizarro_self.custom_output_directory.value = \
self.alter_path(cpprefs.get_default_output_directory())
bizarro_self.default_image_directory.value = \
self.alter_path(cpprefs.get_default_image_directory())
bizarro_self.batch_mode.value = True
pipeline.write_pipeline_measurement(m)
orig_pipeline.write_pipeline_measurement(m, user_pipeline=True)
#
# Write the path mappings to the batch measurements
#
m.write_path_mappings(
[(mapping.local_directory.value, mapping.remote_directory.value)
for mapping in self.mappings])
return h5_path
finally:
m.close()
def save_pipeline(self, workspace, outf=None):
'''Save the pipeline in Batch_data.mat
Save the pickled image_set_list state in a setting and put this
module in batch mode.
if outf is not None, it is used as a file object destination.
'''
from cellprofiler.utilities.version import version_number
if outf is None:
if self.wants_default_output_directory.value:
path = cpprefs.get_default_output_directory()
else:
path = cpprefs.get_absolute_path(self.custom_output_directory.value)
h5_path = os.path.join(path, F_BATCH_DATA_H5)
else:
h5_path = outf
image_set_list = workspace.image_set_list
pipeline = workspace.pipeline
m = cpmeas.Measurements(copy = workspace.measurements,
filename = h5_path)
assert isinstance(image_set_list, cpi.ImageSetList)
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(m, cpmeas.Measurements)
pipeline = pipeline.copy()
target_workspace = cpw.Workspace(pipeline, None, None, None,
m, image_set_list,
workspace.frame)
pipeline.prepare_to_create_batch(target_workspace, self.alter_path)
bizarro_self = pipeline.module(self.module_num)
bizarro_self.revision.value = version_number
if self.wants_default_output_directory:
bizarro_self.custom_output_directory.value = \
self.alter_path(cpprefs.get_default_output_directory())
bizarro_self.default_image_directory.value = \
self.alter_path(cpprefs.get_default_image_directory())
bizarro_self.batch_mode.value = True
pipeline.write_pipeline_measurement(m)
del m
def save_pipeline(self, workspace, outf=None):
'''Save the pipeline in Batch_data.mat
Save the pickled image_set_list state in a setting and put this
module in batch mode.
if outf is not None, it is used as a file object destination.
'''
from cellprofiler.utilities.get_revision import version
if outf is None:
if self.wants_default_output_directory.value:
path = cpprefs.get_default_output_directory()
else:
path = cpprefs.get_absolute_path(self.custom_output_directory.value)
h5_path = os.path.join(path, F_BATCH_DATA_H5)
else:
h5_path = outf
image_set_list = workspace.image_set_list
pipeline = workspace.pipeline
m = cpmeas.Measurements(copy = workspace.measurements,
filename = h5_path)
assert isinstance(image_set_list, cpi.ImageSetList)
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(m, cpmeas.Measurements)
pipeline = pipeline.copy()
target_workspace = cpw.Workspace(pipeline, None, None, None,
m, image_set_list,
workspace.frame)
pipeline.prepare_to_create_batch(target_workspace, self.alter_path)
bizarro_self = pipeline.module(self.module_num)
bizarro_self.revision.value = version
if self.wants_default_output_directory:
bizarro_self.custom_output_directory.value = \
self.alter_path(cpprefs.get_default_output_directory())
bizarro_self.default_image_directory.value = \
self.alter_path(cpprefs.get_default_image_directory())
bizarro_self.batch_mode.value = True
pipeline.write_pipeline_measurement(m)
del m
