#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on May 13 2018
@author: kushal
Chatzigeorgiou Group
Sars International Centre for Marine Molecular Biology
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
"""
from ...common.qdialogs import *
from ..core.common import ViewerUtils
from ..core import organize_metadata
from inspect import getmembers, isfunction
from .pytemplates.tiff_io_pytemplate import *
from ..core.viewer_work_environment import ViewerWorkEnv
import os
from functools import partial
[docs]class ModuleGUI(QtWidgets.QDockWidget):
load_methods = ['asarray', 'asarray-multi', 'imread']
def __init__(self, parent, viewer_reference):
self.vi = ViewerUtils(viewer_reference)
QtWidgets.QDockWidget.__init__(self, parent)
self.ui = Ui_DockWidget()
self.ui.setupUi(self)
self.ui.btnSelectTiff.clicked.connect(self.select_tiff_file)
self.ui.btnSelectMetaFile.clicked.connect(self.select_meta_file)
self.ui.btnLoadIntoWorkEnv.clicked.connect(self.load_tiff_file_slot)
self.ui.radioButtonAsArray.clicked.connect(partial(self.set_load_method, 'asarray'))
self.ui.radioButtonAsArrayMulti.clicked.connect(partial(self.set_load_method, 'asarray-multi'))
self.ui.radioButtonImread.clicked.connect(partial(self.set_load_method, 'imread'))
self._tiff_file_path = None
self._meta_file_path = None
self._load_method = None
# all available meta data loaders
meta_funcs = [f for f in getmembers(organize_metadata) if isfunction(f[1])]
self.meta_loaders = dict(
zip(
[f[0] for f in meta_funcs], # function name
[f[1].__doc__ for f in meta_funcs] # function extension from docstring
)
)
self.ui.listWidget_meta_data_loader.addItems(self.meta_loaders.keys())
self.ui.listWidget_meta_data_loader.currentItemChanged.connect(self.check_meta_path)
self.meta_loader = None
@property
def tiff_file_path(self) -> str:
return self._tiff_file_path
@tiff_file_path.setter
def tiff_file_path(self, path: str):
self._tiff_file_path = path
self.ui.labelFileTiff.setText(self.tiff_file_path)
@property
def meta_file_path(self) -> str:
return self._meta_file_path
@meta_file_path.setter
def meta_file_path(self, path: str):
self._meta_file_path = path
self.ui.labelFileMeta.setText(self.meta_file_path)
def get_load_method(self) -> str:
if self._load_method is None:
raise ValueError('Load method not set.')
else:
return self._load_method
def set_load_method(self, method: str):
if method not in self.load_methods:
raise ValueError('Must set one of the following methods: imread, asarray, asarray-multi.')
self._load_method = method
@use_open_file_dialog('Choose tiff file', '', ['*.tiff', '*.tif'])
def select_tiff_file(self, path, *args, **kwargs):
self.tiff_file_path = path
self.check_meta_path()
@use_open_file_dialog('Choose meta data file', '')
def select_meta_file(self, path, *args, **kwargs):
if self.meta_loader is not None:
ext = self.meta_loaders[self.meta_loader]
if not path.endswith(ext):
QtWidgets.QMessageBox.information(
self.parent(),
f'File extension mismatch',
f'The file extension of the chosen meta data file does not match '
f'the expected file extension <{ext}> for the format <{self.meta_loader}>\n\n'
f'You can still try to load the meta data from this file.',
QtWidgets.QMessageBox.Ok
)
self.meta_file_path = path
@present_exceptions('Could not open file(s)', 'The following error occurred while trying to open the image file.')
def load_tiff_file_slot(self, *args, **kwargs):
tiff_path = self.tiff_file_path
if not tiff_path:
raise ValueError('Nothing to load, you must choose a file to load.')
method = self.get_load_method()
if self.ui.radioButton_axes_custom.isChecked():
axes_order = self.ui.lineEdit_axes_custom.text()
else:
axes_order = None
if self.ui.groupBox_meta_loader.isChecked():
if self.meta_file_path is None:
raise AttributeError(
"You have not chosen a meta data file.\n"
"Uncheck 'Load meta data' if you do not wish to load "
"meta data through this module"
)
if self.meta_loader is None:
raise AttributeError(
"You have not selected a meta data format"
)
meta_path = self.meta_file_path
meta_format = self.meta_loader
else:
meta_path = None
meta_format = None
self.load(tiff_path, method, axes_order, meta_path, meta_format=meta_format)
[docs] def load(
self,
tiff_path: str,
method: str,
axes_order: Optional[str] = None,
meta_path: Optional[str] = None,
meta_format: Optional[str] = None
) -> ViewerWorkEnv:
"""
Load a tiff file along with associated meta data
:param tiff_path: path to the tiff file
:param meta_path: path to the json meta data file
:param method: one of "asarray", "asarray-multi", or "imread"
"asarray" and "asarray-multi" uses :meth:`tifffile.asarray`
"asarray-multi" is for multi-page tiffs
"imread" uses :meth:`tifffile.imread`
:param axes_order: axes order, examples: txy, xyt, tzxy, xytz etc.
:param meta_format: name of function from viewer.core.organize_meta that should be used
to organize the meta data.
"""
self.vi.viewer.status_bar_label.showMessage('Please wait, loading tiff file, this may take a few minutes...')
if not self.vi.discard_workEnv():
return
self.vi.viewer.workEnv = ViewerWorkEnv.from_tiff(
path=tiff_path,
method=method,
meta_path=meta_path,
axes_order=axes_order,
meta_format=meta_format
)
self.vi.update_workEnv()
self.vi.enable_ui(True)
self.vi.viewer.ui.label_curr_img_seq_name.setText(os.path.basename(tiff_path))
self.vi.viewer.status_bar_label.showMessage('File loaded into work environment!')
return self.vi.viewer.workEnv