def get_neox_args(context):
args = AttrMap(context.get_hparams())
exp_config = context.get_experiment_config()
# Gather overrides.
overwrite_values = args.pop("overwrite_values")
# We are going to overwrite certain neox_args with determined config values
# from the experiment config to ensure consistency.
assert ("batches" in exp_config["searcher"]["max_length"]
), "Please specify max_length in batches."
assert ("batches" in exp_config["min_validation_period"]
), "Please specify min_validation_period in batches."
overwrite_values.update({
"train_iters":
exp_config["searcher"]["max_length"]["batches"],
"save_interval":
exp_config["min_validation_period"]["batches"],
"eval_interval":
exp_config["min_validation_period"]["batches"],
"global_num_gpus":
context.distributed.get_size(),
"seed":
context.env.trial_seed,
})
for k, v in overwrite_values.items():
logging.info(f"Setting neox_args.{k} to {v}")
# Build neox args.
neox_args = NeoXArgs.process_parsed_deepy_args(
args, overwrite_values=overwrite_values)
return neox_args
def configJobInternal(config):
# Get cluster config values
# Cluster section is ignored, add it again
d = AttrMap( config )
# remove "config" value and convert boolean flags to strings again,
# these config is used only with strings in the generator
d.pop("config")
config = AttrMap( { "Cluster" : d } )
# add the modules path of this file, which can be used in the (.ini files)
# and also the execDir of the submit.py
config["General"] = {
"configuratorModuleDir" : configuratorModuleDir,
"configuratorModulePath" : configuratorModulePath,
"currentWorkDir" : os.getcwd(),
"jobDir" : os.path.dirname(os.path.abspath(config.Cluster.jobGeneratorConfig)),
"configureScriptArgs" : " ".join(sys.argv)
}
config.Cluster.jobGeneratorOutputDir = os.path.abspath(config.Cluster.jobGeneratorOutputDir )
# load generator module dyanamically and start the job generator
# load the given Cluster.jobGenerator class
module, generatorClass = iH.importClassFromModuleString(config.Cluster.jobGenerator, verbose=True)
gen = generatorClass(config)
gen.generate()
return 0
def __init__(self, name=None, **fields):
global NEXT_RESOURCE_NUM
if name is not None:
fields["name"] = name
if "name" not in fields:
fields["name"] = "resource-%d" % NEXT_RESOURCE_NUM
NEXT_RESOURCE_NUM += 1
fields['tags'] = Tags(fields.get('tags', []))
AttrMap.__init__(self, fields)
def get_stats(root: Any) -> AttrMap:
"""
Выдаем статистику
:return: {stats: [dict(name, score) for user], me: position}
"""
return AttrMap(request('stats', login=root.LOGIN))
def sign_in(root: Any, _locals: dict, login: str, password: str,
password2: str):
"""
Регистрация пользователя
"""
if login == '':
_locals['entry_login'].focus()
root.Alert.show('Введите логин')
elif len(login) > 20:
_locals['entry_login'].focus()
root.Alert.show('Логин не должен быть длиннее 20 символов')
elif password == '':
_locals['entry_password'].focus()
root.Alert.show('Введите пароль')
elif password2 == '':
_locals['entry_password2'].focus()
root.Alert.show('Повторите пароль')
elif password != password2:
root.Alert.show('Пароли не совпадают')
elif (response := request('sing_in', login=login,
password=password))['response']:
if os.path.exists('.auth'):
os.remove('.auth')
with open('.auth', 'w') as data:
data.write(f'{response["login"]}::{password}')
subprocess.check_call(['attrib', '+H', '.auth'])
root.LOGIN = response['login']
root.USER_NAME, root.USER_ID = response['login'].split('#')
root.profile = AttrMap(request(f'profile/{root.USER_ID}'))
root.history_view(_locals=_locals)
def _get_obs(self):
cam_color, cam_depth = self.camera.get_image()
# update objects positions registered with digits
self.digits.update()
colors, depths = self.digits.render()
obj_pose = self.obj.get_base_pose()
return AttrMap({
"camera": {
"color": cam_color,
"depth": cam_depth
},
"digits": [{
"color": color,
"depth": depth
} for color, depth in zip(colors, depths)],
"robot":
self.robot.get_states(),
"object": {
"position": np.array(obj_pose[0]),
"orientation": np.array(obj_pose[1]),
},
})
def upward_wrapper(self):
childrens_attrs = {}
for k, v in self.children().items():
attr = getattr(v, func.__name__)
if callable(attr):
childrens_attrs[k] = attr()
else:
childrens_attrs[k] = attr
self_attrs = func(self)
intersection = set(childrens_attrs.keys()).intersection(self_attrs.keys())
if intersection:
raise AttributeError(
f"Found keys {intersection} in both childrens_attrs and self_attrs"
)
attrs = {**childrens_attrs, **self_attrs}
attrs = _remove_empty_dict_leaf(attrs)
# TODO(poweic): It's confusing to have both SpaceDict & AttrMap at the same
# time. Also, return AttrMap in new() method of SpaceDict is weird.
# Consider creating that's both SpaceDict and AttrMap at the same time.
if func.__name__ == "get_states":
attrs = AttrMap(attrs)
else:
attrs = SpaceDict(attrs)
return attrs
def load(self, path):
with open(path, "rb") as f:
custom = yaml.safe_load(f)
custom = AttrMap(custom)
for attr in self._config:
if attr in custom:
self._config[attr].update(custom[attr])
def complete_quest(root: Any, quest_data: "interface.QuestProcess"):
"""
Сохраняем результаты тестирования
"""
root.profile = AttrMap(
request(f'profile/{root.USER_ID}/quest/{quest_data.quest.name}',
completed_count=f'{quest_data.completed_count}',
score=f'{quest_data.score}',
answers=f'[{quest_data.answers}]'))
def _main(root: Any, _locals: dict = None):
if LOGIN and PASSWORD and USER_NAME and USER_ID:
if request('auth', login=LOGIN, password=PASSWORD)['response']:
root.profile = AttrMap(request(f'profile/{USER_ID}'))
root.home_view(_locals=_locals)
else:
os.remove('.auth')
root.log_in_view(_locals=_locals)
else:
request('test')
root.log_in_view(_locals=_locals)
def __init__(self, name=None, **fields):
"""
Construct a resource with the specified attributes.
Parameters
----------
name : string
Name of the resource. It must be unique to the collection. If it is
not specified, a unique name is generated.
**fields : string -> strings, dicts, and lists
Other fields in the resource.
"""
global NEXT_RESOURCE_NUM
if name is not None:
fields["name"] = name
if "name" not in fields:
fields["name"] = "resource-%d" % NEXT_RESOURCE_NUM
NEXT_RESOURCE_NUM += 1
fields['tags'] = Tags(fields.get('tags', []))
AttrMap.__init__(self, fields)
def _load_untrusted_json(json_str):
try:
obj = json.loads(json_str, parse_int=int, parse_constant=bool)
if (obj['klass'] == 'Command' and isinstance(obj['type'], str)
and (obj['params'] is None or isinstance(obj['params'], dict))
and isinstance(obj['nth_turn'], int)):
return AttrMap(obj)
except Exception as e:
logger.debug('[S] Failed to decode json.')
logger.debug(str(e))
return None
def __init__(self, context: DeepSpeedTrialContext) -> None:
self.context = context
self.exp_config = self.context.get_experiment_config()
self.args = AttrMap(self.context.get_hparams())
# Initalize and get arguments, timers, and Tensorboard writer.
try:
self.neox_args = get_neox_args(self.context)
except:
traceback.print_exc()
raise InvalidHP("Could not parse neox_args.")
self.wrapped_writer = TorchWriter()
self.neox_args.tensorboard_writer = self.wrapped_writer.writer
self.neox_args.configure_distributed_args()
# The tokenizer needs to be built before model initialization in order to set the
# required padded_vocab_size argument.
self.neox_args.build_tokenizer()
megatron_train.initialize_megatron(neox_args=self.neox_args)
self.timers = megatron_utils.Timers(
use_wandb=False,
tensorboard_writer=self.neox_args.tensorboard_writer)
# Model, optimizer, and learning rate.
self.timers("model and optimizer").start()
(
model,
self.optimizer,
self.lr_scheduler,
) = megatron_train.setup_model_and_optimizer(neox_args=self.neox_args)
self.model = self.context.wrap_model_engine(model)
self.timers("model and optimizer").stop()
# Print setup timing.
megatron_utils.print_rank_0("done with setups ...")
self.timers.log(["model and optimizer"])
megatron_utils.print_rank_0("training ...")
# For tracking.
if not self.args.search_world_size:
self.reducer = self.context.wrap_reducer(LMReducers(
self.neox_args),
for_training=False,
for_validation=True)
self.report_memory_flag = True
self.total_train_loss_dict = {}
self.total_val_loss_dict = {}
self.tflops = 0
self.reported_flops = False
self.overflow_monitor = megatron_utils.OverflowMonitor(self.optimizer)
self.noise_scale_logger = megatron_utils.get_noise_scale_logger(
self.neox_args)
self.timers("interval time").start()
def test_mutable():
"""
注意: AttrDict中的sequence type会自动转化为tuple, 即非mutable的形式。也就是
对list中的对象无法修改。如果想要允许对list中的对象进行修改, 需要使用AttrMap,
并指定 ``sequence_type = list``。
"""
user_data = {
"id": "EN-0001",
"phone_numbers": [
{"label": "home", "number": "111-222-3333"},
{"label": "work", "number": "444-555-6666"},
{"label": "mobile", "number": "777-888-9999"},
],
"profile": {
"SSN": "123-45-6789",
"drivers_license": {
"state": "DC",
"license_number": "DC-1234-5678",
}
}
}
user = AttrMap(user_data, sequence_type=list)
assert user.id == "EN-0001"
assert user["id"] == "EN-0001"
user.id = "EN-0002"
assert user.id == "EN-0002"
assert user["id"] == "EN-0002"
# nested dict is also attrdict
assert user.phone_numbers[0].number == "111-222-3333"
assert user.phone_numbers[0]["number"] == "111-222-3333"
user.phone_numbers[0].number = "111-111-1111"
assert user.phone_numbers[0].number == "111-111-1111"
assert user.phone_numbers[0]["number"] == "111-111-1111"
def test_invalid_name():
user_data = {
"_id": 1,
"first name": "John",
"last name": "David",
"email": "*****@*****.**",
}
user = AttrMap(user_data, sequence_type=list)
# 无法用 dict.attr 的风格访问
with pytest.raises(Exception):
user._id
# 但仍可以用 dict[attr] 的风格访问
assert user["_id"] == 1
def test_coco():
# ignore warnings in this test
warnings.simplefilter('ignore')
# args
args = AttrMap({
'epochs': 1,
'steps': 1,
'imagenet_weights': False,
'snapshots': False,
'dataset_type': 'coco',
'coco_path': 'tests/test-data/coco',
})
# run training / evaluation
keras_retinanet.bin.train.main_(args)
def test_csv():
# ignore warnings in this test
warnings.simplefilter('ignore')
args = AttrMap({
'epochs': 1,
'steps': 1,
'imagenet_weights': False,
'snapshots': False,
'dataset_type': 'csv',
'annotations': 'tests/test-data/csv/annotations.csv',
'classes': 'tests/test-data/csv/classes.csv'
})
# run training / evaluation
keras_retinanet.bin.train.main_(args)
def test_vgg():
# ignore warnings in this test
warnings.simplefilter('ignore')
args = AttrMap({
'backbone': 'vgg16',
'epochs': 1,
'steps': 1,
'imagenet_weights': False,
'snapshots': False,
'freeze_backbone': True,
'dataset_type': 'coco',
'coco_path': 'tests/test-data/coco'
})
# run training / evaluation
keras_retinanet.bin.train.main_(args)
def __init__(
self,
message: Optional[int] = None,
*,
peer_id: Optional[int] = None,
random_id: Optional[int] = None,
user_id: Optional[int] = None,
domain: Optional[str] = None,
chat_id: Optional[int] = None,
user_ids: Optional[List[int]] = None,
peer_ids: Optional[List[int]] = None,
lat: Optional[float] = None,
long: Optional[float] = None,
attachment: Optional[List[str]] = None,
reply_to: Optional[int] = None,
forward_messages: Optional[List[int]] = None,
sticker_id: Optional[int] = None,
group_id: Optional[int] = None,
keyboard: Optional[str] = None,
payload: Optional[str] = None,
dont_parse_links: Optional[bool] = None,
disable_mentions: Optional[bool] = None,
intent: Optional[str] = None,
expire_ttl: Optional[int] = None,
silent: Optional[bool] = None,
**kwargs,
):
if random_id is None:
random_id = randint(-2 * 31, 2 * 31)
preload_data = locals().copy()
del preload_data["self"]
kwargs_vals = preload_data.pop("kwargs")
preload_data.update(kwargs_vals)
self._params = AttrMap(
dict(filter(lambda x: x[1] is not None, preload_data.items())))
self._set_path()
self._join_attach()
def log_in(root: Any, _locals: dict, login: str, password: str):
"""
Авторизация пользователя
"""
if login == '':
_locals['entry_login'].focus()
root.Alert.show('Введите логин')
elif password == '':
_locals['entry_password'].focus()
root.Alert.show('Введите пароль')
elif request('auth', login=login, password=password)['response']:
if os.path.exists('.auth'):
os.remove('.auth')
with open('.auth', 'w') as data:
data.write(f'{login}::{password}')
subprocess.check_call(['attrib', '+H', '.auth'])
root.LOGIN = login
root.USER_NAME, root.USER_ID = login.split('#')
root.profile = AttrMap(request(f'profile/{root.USER_ID}'))
root.history_view(_locals=_locals)
else:
root.Alert.show('Неправильный логин или пароль')
G = AttrMap(
{
'APPEND': [],
'ACTIONS': [],
'BUILD': [],
'BUILDER': ["./build-boot-image.py"],
'BUNDLE_FILE': '',
'BUNDLED': 'bundled',
'DEBUG': 0,
'DEFAULT': 'default',
'DRY_RUN': 0,
'EDIT': '',
'BOOT': False,
'EXCLUDES': [],
'FLAGS': [],
'IMAGE': 'boot-image.raw',
'ISO': 'centos.iso',
'LABEL': '',
'MODE': '',
'MODES': ['default'],
'ONLY': [],
'SUPPORTED_VERSION': '1',
'TOPDIR': 'bundled',
'TAR_CLEANUP': [],
'VARS': [],
'VERBOSE': 0,
'STRICT': 1,
'FORMAT': '',
},
sequence_type=list) #,recursive=False)
def __init__(self):
with open(self.DEFAULT, "rb") as f:
default = yaml.safe_load(f)
self._config = AttrMap(default)
log['gen/loss'] = loss_g.item()
log['dis/loss'] = loss_d.item()
logreport(log)
with torch.no_grad():
log_test = test(config, test_data_loader, gen, criterionMSE, epoch)
testreport(log_test)
if epoch % config.snapshot_interval == 0:
checkpoint(config, epoch, gen, dis)
logreport.save_lossgraph()
testreport.save_lossgraph()
if __name__ == '__main__':
with open('config.yml', 'r') as f:
config = yaml.load(f)
config = AttrMap(config)
utils.make_manager()
n_job = utils.job_increment()
config.out_dir = os.path.join(config.out_dir, '{:06}'.format(n_job))
os.makedirs(config.out_dir)
print('Job number: {:04d}'.format(n_job))
shutil.copyfile('config.yml', os.path.join(config.out_dir, 'config.yml'))
train(config)
def main():
""" {old validatation file infos} is compared
to { new validation file infos} ==> outputs new file validation info
"""
parser = MyOptParser()
parser.add_argument("-s", "--searchDirNew", dest="searchDirNew",
help="""This is the search directory where it is looked for output files (.tiff,.exr,.rib.gz). """,
metavar="<path>", default=None, required=False)
parser.add_argument("--valFileInfoGlobNew", dest="valFileInfoGlobNew",
help="""
The globbing expression for all input xmls with file status which
are consolidated into a new file info under --output. The found and validated files in --searchDir (if specified) are
added to the set of new files.
""", default=None, metavar="<glob>", required=False)
parser.add_argument("--valFileInfoGlobOld", dest="valFileInfoGlobOld",
help="""
The globbing expression for all old input xmls with file status which
are consolidated with the new files into a combined file info under --output.
""", default=None, metavar="<glob>", required=False)
parser.add_argument("--pipelineSpecs", dest="pipelineSpecs", default="",
help="""Json file with info about the pipeline, fileValidation, fileValidationTools.
""", metavar="<string>", required=True)
parser.add_argument("--statusFolder", dest="statusFolder", default=None,
help="""The output status folder which contains links to files which are finished, or can be recovered.
""", metavar="<string>", required=False)
parser.add_argument("--validateOnlyLastModified", dest="validateOnlyLastModified", type=cF.toBool, default=True,
help="""The file with the moset recent modified time is only validated, all others are set to finished!.""", required=False)
parser.add_argument("-o", "--output", dest="output",
help="""The output xml which is written, which proivides validation info for each file found""", metavar="<path>", required=True)
try:
print("====================== FileValidation ===========================")
opts= AttrMap(vars(parser.parse_args()))
if not opts.searchDirNew and not opts.valFileInfoGlobNew:
raise ValueError("You need to define either searchDirNew or valFileInfoGlobNew!")
if opts.valFileInfoGlobOld == "":
opts.valFileInfoGlobOld = None
print("searchDir: %s" % opts.searchDirNew)
print("valFileInfoGlobNew: %s" % opts.valFileInfoGlobNew)
print("valFileInfoGlobOld: %s" % opts.valFileInfoGlobOld)
print("output: %s" % opts.output)
d = cF.jsonLoad(opts.pipelineSpecs)
pipelineTools = d["pipelineTools"]
fileValidationSpecs = d["fileValidationSpecs"]
fileValidationTools = d["fileValidationTools"]
valDataAllNew = dict()
deleteFiles = []
# load new validataion datas
if opts.valFileInfoGlobNew is not None:
print("Load new validation files")
valDataAllNew , valFilesNew = loadValidationFiles(opts.valFileInfoGlobNew)
preferGlobalPaths(valDataAllNew)
# add searchDir files to new set
# search files ============================================================================
if opts.searchDirNew is not None:
print("Validate all files in: %s with pipeLineSpecs: %s" % (opts.searchDirNew , opts.pipelineSpecs) )
allFiles = searchFiles(opts.searchDirNew, opts, fileValidationSpecs,fileValidationTools,pipelineTools)
for ha, f in allFiles.items():
if ha in valDataAllNew:
print("""WARNING: File %s already found in validation data set
from globbing expr. %s """ % (f["absPath"], opts.valFileInfoGlobNew))
else:
valDataAllNew[ha] = f
# ===============================================================================================
# load old validation datas
if opts.valFileInfoGlobOld is not None:
print("Load old validation files")
valDataAllOld , valFilesOld = loadValidationFiles(opts.valFileInfoGlobOld)
preferGlobalPaths(valDataAllOld)
# add old to new validatation infos
for ha, valInfo in valDataAllOld.items():
if ha not in valDataAllNew:
# this old file hash is not in our current list, so add it!
# check absPath if it exists otherwise try to extent the relPath with dir of this validation file.
if not os.path.exists(valInfo["absPath"]):
absPath = os.path.join( os.path.dirname(valInfo["validatationInfoPath"]) , valInfo["relPath"] )
if not os.path.exists(absPath):
print(valInfo["validatationInfoPath"])
raise NameError("""File path in valid. info file: %s
does not exist, extended rel. path to: %s does also not exist!""" % (valInfo["absPath"],absPath))
else:
print("Replacing inexisting path %s with %s", valInfo["absPath"], absPath)
valInfo["absPath"] = absPath
# copy element to new file info
valDataAllNew[ha] = valInfo
else:
# we have the same hash in the new info
# take our new one which is better!
# delete old file if it is not linked to by new file
if os.path.realpath(valDataAllNew[ha]["absPath"]) != os.path.realpath(valInfo["absPath"]):
deleteFiles.append(valInfo["absPath"])
# make final list
finalFiles = [ f for f in valDataAllNew.values() ]
printSummary(finalFiles,pipelineTools,False)
print("Make output validation file")
f = open(opts.output,"w+")
cF.jsonDump(finalFiles,f, sort_keys=True)
f.close();
# Renew status folder, move over new xml info
if opts.statusFolder is not None:
print("Renew status folder:")
finished = os.path.join(opts.statusFolder,"finished")
recover = os.path.join(opts.statusFolder,"recover")
cF.makeDirectory(finished,interact=False, defaultMakeEmpty=True)
cF.makeDirectory(recover ,interact=False, defaultMakeEmpty=True)
# make symlinks for all files in the appropriate folder:
paths = {"recover": recover, "finished": finished}
for f in finalFiles:
h = f["hash"]
p = os.path.relpath(f["absPath"],start=paths[f["status"]])
filename = os.path.basename(p)
head,ext = os.path.splitext(filename)
os.symlink(p, os.path.join( paths[f["status"]] , head+"-uuid-"+h+ext ) );
print("=================================================================")
except Exception as e:
print("====================================================================")
print("Exception occured: " + str(e))
print("====================================================================")
traceback.print_exc(file=sys.stdout)
parser.print_help()
return 1
out_rgb = np.clip(out_[:3], -1, 1)
out_cloud = np.clip(out_[3], -1, 1)
allim[0, 0, :] = np.repeat(in_nir[None, :, :], repeats=3,
axis=0) * 127.5 + 127.5
allim[0, 1, :] = in_rgb * 127.5 + 127.5
allim[0, 2, :] = out_rgb * 127.5 + 127.5
allim[0, 3, :] = np.repeat(
out_cloud[None, :, :], repeats=3, axis=0) * 127.5 + 127.5
allim = allim.transpose(0, 3, 1, 4, 2)
allim = allim.reshape((h * p, w * p, c))
save_image(args.out_dir, allim, i, 1, filename=filename)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--config', type=str, required=True)
parser.add_argument('--test_dir', type=str, required=True)
parser.add_argument('--out_dir', type=str, required=True)
parser.add_argument('--pretrained', type=str, required=True)
parser.add_argument('--cuda', action='store_true')
parser.add_argument('--gpu_ids', type=int, default=[0])
parser.add_argument('--manualSeed', type=int, default=0)
args = parser.parse_args()
with open(args.config, 'r') as f:
config = yaml.load(f)
config = AttrMap(config)
predict(config, args)
def process(xmlfile, *xmlfiles, **options):
"""
Main program code.
1. Load XML file.
2. Export structured annotation data from XML to relational database.
3. Save database tables as CSV files.
4. Create polygons from the annotations.
5. Create polygonal selection by adding and subtracting polygons.
6. Save polygonal selection as a binary object.
7. Create binary mask at the specified resolution with the specified
field-of-view (FOV) from the polygonal selection.
8. Export binary mask (values: 0-255) to an 8-bit TIFF file.
+1 (optional): display polygonal selection and binary mask.
"""
p = AttrMap(options)
# Start logging
global logger
temp_logfile = tempfile.mkstemp()
logging.basicConfig(format='[%(asctime)s] %(message)s',
datefmt='%d-%m-%Y %H:%M:%S',
filename=temp_logfile[1],
filemode="w")
logger = logging.getLogger("roi")
logger.setLevel(max(50 - p.verbose, 1))
logger.critical("The program started with the command: {}".format(" ".join(
sys.argv)))
xmlfiles = (xmlfile, ) + xmlfiles
err = 0
for f in xmlfiles:
try:
# Parse data in XML file and create data tables
logger.info("{}".format(f))
if not str(f).lower().endswith(".xml"):
logger.warning("Input does not appear to be an XML file.")
points, regions, annotations = parse_xml(f)
# Create output base name
p.basename = os.path.splitext(os.path.split(f)[-1])[0]
if p.outdir:
if not os.path.isdir(p.outdir):
os.makedirs(p.outdir)
p.outbase = os.path.join(p.outdir, p.basename)
else:
p.outbase = os.path.splitext(f)[0]
# Save the tables of the relational database
if p.csv:
points.to_csv(p.outbase + "_points.csv")
regions.to_csv(p.outbase + "_regions.csv")
annotations.to_csv(p.outbase + "_annotations.csv")
# Retrieve polygons
polygons = create_polygons(points)
# Treat annotation layers separately
for layer in annotations.index.unique():
layerdir = p.outdir or os.path.split(f)[0]
layerdir = os.path.join(
layerdir, "AnnotationLayer_{0:02d}".format(layer))
if not os.path.isdir(layerdir):
os.makedirs(layerdir)
layerbase = os.path.join(layerdir, p.basename)
# Set algebra
selection = create_selection(polygons, regions, layer=layer)
if selection is None:
logger.warning("Annotation layer {} does not have any "
"polygonal selections.".format(layer))
continue
# Display selection
if p.display:
visualise_polygon(selection, show=True, save=False)
# Export the polygonal selection object to a binary file
if p.bin:
with open(layerbase + "_selection.obj", "wb") as fp:
dill.dump(selection, fp)
# Generate binary mask
if p.mask:
if len(p.scale) == 1:
scale_x, scale_y = p.scale * 2 # p.scale is a tuple!
elif len(p.scale) == 2:
scale_x, scale_y = p.scale # p.scale is a tuple!
else:
raise ValueError(
"The number of scaling factors must be 2.")
mask = create_mask(selection,
original_shape=p.original_shape,
target_shape=p.target_shape,
scale_x=scale_x,
dimscale_x=p.dimscale_x,
scale_y=scale_y,
dimscale_y=p.dimscale_y,
tile=p.tile,
fill_value=p.fill_value)
# Display binary mask
if p.display:
plt.imshow(mask, cmap="gray", aspect="equal")
plt.show()
# Save binary mask
Image.fromarray(mask).save(
os.path.join(layerbase + "_mask.tif"))
# Save the corresponding histology image
if p.histo:
histo = create_histo(img=p.image,
dimlevel=p.dimlevel,
original_shape=p.original_shape,
target_shape=p.target_shape,
scale_x=scale_x,
dimscale_x=p.dimscale_x,
scale_y=scale_y,
dimscale_y=p.dimscale_y,
tile=p.tile)
Image.fromarray(histo).save(
os.path.join(layerbase + "_histo.tif"))
except Exception as exc:
logger.critical("FAILURE: {}. Exception: {}".format(
f, exc.args[0]))
err += 1
continue
# Conclude run
if err == 0:
logger.critical("All tasks were successfully completed.")
else:
logger.critical("Tasks were completed with {} error(s).".format(err))
# Save logs
try:
shutil.copy(temp_logfile[1], p.outbase + ".log")
except PermissionError:
pass
def test_add_fragment_urls(mock_log_change):
# Ensure shelfmark not existing is properly handled.
command = add_fragment_urls.Command()
row = AttrMap({"shelfmark": "mm", "url": "example.com"})
command.add_fragment_urls(row) # Test would fail if error were raised
assert command.stats["not_found"] == 1
assert not mock_log_change.call_count
# Ensure that the iiif url is not overwritten unless overwrite arg is provided
command = add_fragment_urls.Command()
command.overwrite = None
command.dryrun = None
orig_frag = Fragment.objects.create(
shelfmark="T-S NS 305.66",
iiif_url="https://cudl.lib.cam.ac.uk/iiif/MS-TS-NS-J-00490",
)
row = AttrMap({
"shelfmark": orig_frag.shelfmark,
"url": "https://cudl.lib.cam.ac.uk/view/MS-TS-NS-J-00600",
})
command.add_fragment_urls(row)
fragment = Fragment.objects.get(shelfmark=orig_frag.shelfmark)
assert fragment.url == row["url"]
assert fragment.iiif_url == orig_frag.iiif_url
assert command.stats["url_added"] == 1
assert not command.stats["iiif_added"]
assert not command.stats["iiif_updated"]
assert not command.stats["url_updated"]
mock_log_change.assert_called_with(fragment, "added URL")
command = add_fragment_urls.Command()
command.overwrite = True
command.dryrun = None
orig_frag = Fragment.objects.create(
shelfmark="T-S NS 305.75",
iiif_url="https://cudl.lib.cam.ac.uk/iiif/MS-TS-NS-J-00490",
)
row = AttrMap({
"shelfmark": orig_frag.shelfmark,
"url": "https://cudl.lib.cam.ac.uk/view/MS-TS-NS-J-00600",
})
command.add_fragment_urls(row)
fragment = Fragment.objects.get(shelfmark=orig_frag.shelfmark)
assert fragment.iiif_url != orig_frag.iiif_url
assert fragment.iiif_url == "https://cudl.lib.cam.ac.uk/iiif/MS-TS-NS-J-00600"
assert command.stats["iiif_updated"] == 1
mock_log_change.assert_called_with(fragment,
"added URL and updated IIIF URL")
# test updating url — url matches, should skip
fragment.url = row.url
fragment.save()
command.stats = defaultdict(int)
command.add_fragment_urls(row)
assert not command.stats["url_updated"]
assert not command.stats["url_added"]
assert command.stats["skipped"] == 1
# fragment url is set but does not match, no overwrite
fragment.url = "http://example.com/fragment/view"
fragment.save()
command.overwrite = False
command.stats = defaultdict(int)
command.add_fragment_urls(row)
assert not command.stats["url_updated"]
assert not command.stats["url_added"]
assert command.stats["skipped"] == 1
# url mismatch, overwrite specified
command.overwrite = True
command.stats = defaultdict(int)
command.add_fragment_urls(row)
assert command.stats["url_updated"] == 1
assert not command.stats["url_added"]
assert not command.stats["skipped"]
# Ensure that changes aren't saved if dryrun argument is provided
mock_log_change.reset_mock()
command = add_fragment_urls.Command()
command.overwrite = None
command.dryrun = True
orig_frag = Fragment.objects.create(
shelfmark="T-S NS 305.80",
iiif_url="https://cudl.lib.cam.ac.uk/iiif/MS-TS-NS-J-00490",
)
row = AttrMap({
"shelfmark": orig_frag.shelfmark,
"url": "https://cudl.lib.cam.ac.uk/view/MS-TS-NS-J-00600",
})
command.add_fragment_urls(row)
fragment = Fragment.objects.get(shelfmark=orig_frag.shelfmark)
assert fragment.iiif_url == orig_frag.iiif_url
assert not mock_log_change.call_count
import os
import sys
import yaml
from attrdict import AttrMap
current_dir = os.path.dirname(os.path.abspath(__file__))
with open(current_dir + '/settings.yml', 'r') as stream:
config = yaml.load(stream, Loader=yaml.FullLoader)
sys.modules[__name__] = AttrMap(config)
def new(self):
# TODO(poweic): instead of None, use torch.Tensor? (placeholder + strict schema)
return AttrMap({
k: v.new() if isinstance(v, collections.abc.Mapping) else None
for k, v in self.spaces.items()
})
def get_children_states(self):
return AttrMap(
_remove_empty_dict_leaf(
{k: v.get_states() for k, v in self.children().items()}
)
)
