def test_external_image_selection(self):
d = tempfile.mkdtemp(prefix='external_image', dir='.')
self.general_setup(d)
os.mkdir(os.path.join(d, 'test_projects'))
os.mkdir(os.path.join(d, 'images'))
hdf5dir = os.path.join(d, 'hdf5')
def mysetup():
os.mkdir(hdf5dir)
with open(os.path.join(hdf5dir, 'test_project1.hdf5'), 'w') as fp:
fp.write('foo')
mysetup()
self.addFileToRemove(d, preemptive=False)
be = batch_project.BatchExecutor(os.path.join(d, 'test_projects'),
workdir=d,
global_variables={'image_dir': os.path.join(d, 'images'),
'hdf5dir': hdf5dir,
'results': os.path.join(d, 'images')})
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile('tests/specifications/external_image_batch_process.json'))
saveAsPng(self.locateFile('tests/images/test_project1.jpg'),
os.path.join(d, 'images', 'test_project1.png'.format(d)))
with open(os.path.join(d, 'images', 'arguments.csv'), 'w') as fp:
fp.write('test_project1.png,no,16')
dir, name = be.runProjectLocally(batchProject)
be.finish(remove_logs=True)
self.assertTrue(dir is not None)
self.assertTrue(os.path.exists(os.path.join(hdf5dir, 'test_project1.hdf5')))
def test_runwithpermutation(self):
self.addFileToRemove('imageset.txt', preemptive=True)
with open('imageset.txt', 'w') as fp:
fp.writelines([
filename + os.linesep
for filename in os.listdir(self.locateFile('tests/images'))
if not filename.startswith('test_project')
])
if os.path.exists('test_projects'):
shutil.rmtree('test_projects')
os.mkdir('test_projects')
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile(
'tests/specifications/permutation_batch_process.json'))
global_state = {
'projects': 'test_projects',
'project': batchProject,
'picklists_files': {},
'image_dir': self.locateFile('tests/images'),
'count': batch_project.IntObject(20),
'permutegroupsmanager': PermuteGroupManager()
}
batchProject.loadPermuteGroups(global_state)
for i in range(100):
batchProject.executeOnce(global_state)
self.assertTrue(global_state['permutegroupsmanager'].hasNext())
def test_extend(self):
batch_project.loadCustomFunctions()
import shutil
self.addFileToRemove('testimages_extend', preemptive=True)
shutil.copytree(os.path.dirname(self.locateFile('./images/sample.json')), 'testimages_extend')
self.assertTrue(processSpecification(self.locateFile('tests/specifications/batch_extension_process.json'), '',
'testimages_extend', skipValidation=True) == 1)
def test_run(self):
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile('tests/specifications/batch_process.json'))
be = self.createExecutor('main_batch_run',
skipValidation=True,
loglevel=10,
setup=True,
global_variables={
'image_dir':
self.locateFile('tests/images'),
'donorImages':
self.locateFile('tests/images')
})
be.runProjectLocally(batchProject)
be.runProjectLocally(batchProject)
global_state = be.initialState
try:
# self.assertFalse(global_state['permutegroupsmanager'].hasNext())
global_state['permutegroupsmanager'].next()
self.assertTrue(global_state['permutegroupsmanager'].hasNext())
global_state['permutegroupsmanager'].next()
self.fail('Should have seen an end of resource exception')
except EndOfResource:
pass
be.finish(remove_logs=True)
def test_image_selection(self):
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile('tests/specifications/simple_image_selector_plugin.json'))
be = self.createExecutor('image_selection', skipValidation=True, setup=True, loglevel=10,
global_variables={'image_dir': self.locateFile('tests/images')})
dir, name = be.runProjectLocally(batchProject)
be.finish(remove_logs=True)
self.assertTrue(dir is not None)
def general_setup(self, dir):
f = os.path.join(dir, 'imageset.txt')
self.addFileToRemove(f, preemptive=True)
with open(f, 'w') as fp:
fp.writelines([filename + os.linesep for filename in os.listdir(self.locateFile('tests/images')) if
not filename.startswith('test_project')])
f = os.path.join(dir, 'donorset.txt')
self.addFileToRemove(f, preemptive=True)
with open(f, 'w') as fp:
fp.writelines([filename + os.linesep for filename in os.listdir(self.locateFile('tests/images')) if
not filename.startswith('test_project')])
batch_project.loadCustomFunctions()
def test_image_selection(self):
self.general_setup()
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile(
'tests/specifications/simple_image_selector_plugin.json'))
be = batch_project.BatchExecutor(
'test_projects',
skipValidation=True,
global_variables={'image_dir': self.locateFile('tests/images')})
dir, name = be.runProjectLocally(batchProject)
be.finish()
self.assertTrue(dir is not None)
def general_setup(self):
self.addFileToRemove('imageset.txt', preemptive=True)
with open('imageset.txt', 'w') as fp:
fp.writelines([
filename + os.linesep
for filename in os.listdir(self.locateFile('tests/images'))
if not filename.startswith('test_project')
])
self.addFileToRemove('donorset.txt', preemptive=True)
with open('donorset.txt', 'w') as fp:
fp.writelines([
filename + os.linesep
for filename in os.listdir(self.locateFile('tests/images'))
if not filename.startswith('test_project')
])
if os.path.exists('test_projects'):
shutil.rmtree('test_projects')
os.mkdir('test_projects')
batch_project.loadCustomFunctions()
def test_run(self):
if os.path.exists('test_coco_projects'):
shutil.rmtree('test_coco_projects')
os.mkdir('test_coco_projects')
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
'tests/other_plugins/CocoMaskSelector/batch_process.json')
global_state = {
'projects': 'test_coco_projects',
'project': batchProject,
'picklists_files': {},
'workdir': '.',
'coco.annotations':
'tests/other_plugins/CocoMaskSelector/annotations.json',
'count': batch_project.IntObject(20),
'permutegroupsmanager': PermuteGroupManager()
}
global_state.update(createBatchProjectGlobalState(global_state))
batchProject.loadPermuteGroups(global_state)
batchProject.executeOnce(global_state)
def test_external_image_selection(self):
self.addFileToRemove('imageset.txt', preemptive=True)
with open('imageset.txt', 'w') as fp:
fp.writelines([
filename + os.linesep
for filename in os.listdir(self.locateFile('tests/images'))
if not filename.startswith('test_project1')
])
if os.path.exists('results'):
shutil.rmtree('results')
if os.path.exists('test_projects'):
shutil.rmtree('test_projects')
os.mkdir('test_projects')
os.mkdir('test_projects/hdf5')
with open('test_projects/hdf5/test_project1.hdf5', 'w') as fp:
fp.write('foo')
be = batch_project.BatchExecutor('test_projects',
global_variables={
'image_dir':
self.locateFile('tests/images'),
'hdf5dir':
'test_projects/hdf5'
})
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile(
'tests/specifications/external_image_batch_process.json'))
self.addFileToRemove('results', preemptive=True)
self.addFileToRemove('test_projects', preemptive=False)
os.mkdir('results')
saveAsPng(self.locateFile('tests/images/test_project1.jpg'),
'results/test_project1.png')
with open('results/arguments.csv', 'w') as fp:
fp.write('test_project1.png,no,16')
dir, name = be.runProjectLocally(batchProject)
be.finish()
self.assertTrue(dir is not None)
self.assertTrue(
os.path.exists('test_projects/test_project1/test_project1.hdf5'))
def test_runwithpermutation(self):
batch_project.loadCustomFunctions()
d = tempfile.mkdtemp(prefix='external_image', dir='.')
self.general_setup(d)
os.mkdir(os.path.join(d, 'test_projects'))
batch_project.loadCustomFunctions()
batchProject = batch_project.loadJSONGraph(
self.locateFile('tests/specifications/permutation_batch_process.json'))
global_state = {
'projects': os.path.join(d, 'test_projects'),
'project': batchProject,
'workdir': d,
'picklists_files': {},
'image_dir': self.locateFile('tests/images'),
'count': batch_project.IntObject(20),
'permutegroupsmanager': PermuteGroupManager(d)
}
batchProject.loadPermuteGroups(global_state)
for i in range(10):
batchProject.executeOnce(global_state)
self.assertTrue(global_state['permutegroupsmanager'].hasNext())