def _load_dataset_and_samples(self):
""" """
try:
datasets = plankton_core.PlanktonCounterManager(
).get_dataset_names()
for dataset in datasets:
samples = plankton_core.PlanktonCounterManager(
).get_sample_names(dataset)
for sample in samples:
datasetsample = dataset + ': ' + sample
self._datasetsample_dict[datasetsample] = (dataset, sample)
#
self._datasetsample_list.addItems(
sorted(self._datasetsample_dict.keys()))
#
except Exception as e:
debug_info = self.__class__.__name__ + ', row ' + str(
sys._getframe().f_lineno)
toolbox_utils.Logging().error('Exception: (' + debug_info + '): ' +
str(e))
def _change_sample_name(self):
""" """
try:
self.save_data()
dialog = RenameSampleDialog(self, self._current_sample)
if dialog.exec_():
new_sample_name = dialog.get_new_sample_name()
if new_sample_name:
self.save_data()
plankton_core.PlanktonCounterManager().rename_sample(
self._current_dataset, self._current_sample,
new_sample_name)
# Close dialog.
self._parentwidget.reject()
#
except Exception as e:
debug_info = self.__class__.__name__ + ', row ' + str(
sys._getframe().f_lineno)
toolbox_utils.Logging().error('Exception: (' + debug_info + '): ' +
str(e))
def _copy_sample_info_from(self):
""" """
try:
dialog = CopyFromTemplateDialog(self)
if dialog.exec_():
dataset = dialog.get_dataset()
sample = dialog.get_sample()
if dataset and sample:
dir_path = plankton_core.PlanktonCounterManager(
).get_dataset_dir_path()
sample_object = plankton_core.PlanktonCounterSample(
dir_path, dataset, sample)
metadata_dict = sample_object.get_sample_info()
self._from_dict_to_fields(metadata_dict)
#
except Exception as e:
debug_info = self.__class__.__name__ + ', row ' + str(
sys._getframe().f_lineno)
toolbox_utils.Logging().error('Exception: (' + debug_info + '): ' +
str(e))
def __init__(self, parentwidget, dataset, sample):
""" """
self._current_dataset = dataset
self._current_sample = sample
# Create sample object.
dir_path = plankton_core.PlanktonCounterManager().get_dataset_dir_path(
)
self._current_sample_object = plankton_core.PlanktonCounterSample(
dir_path, self._current_dataset, self._current_sample)
#
super(PlanktonCounterDialog, self).__init__(parentwidget)
self.setWindowTitle("Plankton counter")
#
# self.resize(1500, 900)
self.resize(1500, 845)
# self.resize(1000, 750)
#
self.metadata_widget = None
self.methods_widget = None
self.count_widget = None
self.sample_data_widget = None
self._current_tab_index = 0
#
self._create_content()
def read_excel_file(self, excel_file_path=None):
""" """
if excel_file_path == None:
raise UserWarning('Excel file is missing.')
#
dir_path = plankton_core.PlanktonCounterManager().get_dataset_dir_path(
)
#
if (not excel_file_path) or (not os.path.isfile(excel_file_path)):
raise UserWarning('Excel file does not exists.')
#
self._dataset_metadata = {}
self._sample_info = {}
self._sample_header = []
self._sample_rows = []
self._sample_method_dict = {}
# Dataset metadata as <key>:<value>.
# try:
# tablefilereader = toolbox_utils.TableFileReader(
# excel_file_name = excel_file_path,
# excel_sheet_name = 'dataset_metadata.txt',
# )
# # Merge header and rows. Create dict.
# dataset_metadata = [tablefilereader.header()] + tablefilereader.rows()
# for row in dataset_metadata:
# if len(row) >= 2:
# self._dataset_metadata[row[0].strip()] = row[1].strip()
# except:
# pass
# Sample info as <key>:<value>.
tablefilereader = toolbox_utils.TableFileReader(
excel_file_name=excel_file_path,
excel_sheet_name='sample_info.txt',
)
# Merge header and rows. Create dict from ':'-separated rows.
sample_info = [tablefilereader.header()] + tablefilereader.rows()
for row in sample_info:
if len(row) >= 2:
self._sample_info[row[0].strip()] = row[1].strip()
# Sample data on table format.
tablefilereader = toolbox_utils.TableFileReader(
excel_file_name=excel_file_path,
excel_sheet_name='sample_data.txt',
)
self._sample_header = tablefilereader.header()
self._sample_rows = tablefilereader.rows()
# Sample method on table format.
tablefilereader = toolbox_utils.TableFileReader(
excel_file_name=excel_file_path,
excel_sheet_name='counting_method.txt',
)
self._sample_method_header = tablefilereader.header()
self._sample_method_rows = tablefilereader.rows()
# Create dictionary with method step as key.
self._sample_method_dict = {}
for row in self._sample_method_rows:
method_dict = dict(zip(self._sample_method_header, row))
if 'counting_method_step' in method_dict:
self._sample_method_dict[
method_dict['counting_method_step']] = method_dict
def read_file(self, dataset_name=None, sample_name=None):
""" """
if dataset_name == None:
raise UserWarning('Dataset name is missing.')
if sample_name == None:
raise UserWarning('Sample name is missing.')
#
dir_path = plankton_core.PlanktonCounterManager().get_dataset_dir_path(
)
dataset_path = os.path.join(dir_path, dataset_name)
sample_path = os.path.join(dataset_path, sample_name)
#
if (not dataset_path) or (not os.path.exists(dataset_path)):
raise UserWarning('Dataset files are missing.')
if (not sample_path) or (not os.path.exists(sample_path)):
raise UserWarning('Sample files are missing.')
#
self._dataset_metadata = {}
self._sample_info = {}
self._sample_header = []
self._sample_rows = []
self._sample_method_dict = {}
# Dataset metadata as <key>:<value>.
try:
tablefilereader = toolbox_utils.TableFileReader(
file_path=dataset_path,
text_file_name='dataset_metadata.txt',
)
# Merge header and rows. Create dict.
dataset_metadata = [tablefilereader.header()
] + tablefilereader.rows()
for row in dataset_metadata:
if len(row) >= 2:
self._dataset_metadata[row[0].strip()] = row[1].strip()
except:
pass
# Sample info as <key>:<value>.
tablefilereader = toolbox_utils.TableFileReader(
file_path=sample_path,
text_file_name='sample_info.txt',
)
# Merge header and rows. Create dict from ':'-separated rows.
sample_info = [tablefilereader.header()] + tablefilereader.rows()
for row in sample_info:
if len(row) >= 2:
self._sample_info[row[0].strip()] = row[1].strip()
# Sample data on table format.
tablefilereader = toolbox_utils.TableFileReader(
file_path=sample_path,
text_file_name='sample_data.txt',
)
self._sample_header = tablefilereader.header()
self._sample_rows = tablefilereader.rows()
# Sample method on table format.
tablefilereader = toolbox_utils.TableFileReader(
file_path=sample_path,
text_file_name='counting_method.txt',
)
self._sample_method_header = tablefilereader.header()
self._sample_method_rows = tablefilereader.rows()
# Create dictionary with method step as key.
self._sample_method_dict = {}
for row in self._sample_method_rows:
method_dict = dict(zip(self._sample_method_header, row))
if 'counting_method_step' in method_dict:
self._sample_method_dict[
method_dict['counting_method_step']] = method_dict