Source code for mesmerize.viewer.modules.femtonics_mesc

Module for importing data from MESc HDF5 files created from Femtonics microscopes.

from .pytemplates.femtonics_mesc_template import *
import h5py
from datetime import datetime
import os
from ...common.qdialogs import use_open_file_dialog, present_exceptions
from ..core import ViewerUtils, ViewerWorkEnv
from ..core.data_types import ImgData
from typing import List, Union
from re import sub as regex_sub
from ...pyqtgraphCore import PlotWidget
import numpy as np
from cv2 import bitwise_not

def ascii_to_str(array: np.ndarray):
    Get a string from an array of ascii integers

    :param array: array of integers representing ascii chars
    :return: string represented by the array
    return ''.join(
            chr, filter(None, array)

# Navigator object which helps control the
# user's file navigation through the .mesc file
[docs]class MEScNavigator(QtWidgets.QWidget): # emitted every time the hdf path changes # used by ModuleGUI() to determine if Import Image button should be enabled sig_hpath_changed: QtCore.pyqtSignal = QtCore.pyqtSignal(dict) #: emitted every time the hdf path changes sig_channel_doubleclicked: QtCore.pyqtSignal = QtCore.pyqtSignal(dict) #: emitted when a ``Channel`` or ``Curve`` item is double clicked def __init__(self, parent, list_widgets: List[ListWidget]): """ :param parent: parent dockWidget :param list_widgets: list of ListWidget ui objects, in the following order: [sessions_list_widget, units_list_widget, channels_list_widget] """ QtWidgets.QWidget.__init__(self, parent=parent) self.path: str = '' #: system path to the hdf5 file self.file: h5py.File = None #: h5py file handle self.session: str = '' #: currently selected MSession self.sessions: List[str] = [] #: list of ``MSession`` options available in current file self.listw_sessions: ListWidget = list_widgets[0] #: ui list of ``MSession`` options self.listw_sessions.itemClicked.connect(self.set_session) #: sets the current ``MSession`` self.listw_sessions.currentItemChanged.connect(self.set_session) self.unit: str = '' #: currently selected ``MUnit`` self.units: List[str] = [] #: list of ``MUnit`` options available in current ``MSession`` self.listw_units: ListWidget = list_widgets[1] #: ui list of ``MUnit`` options self.listw_units.itemClicked.connect(self.set_unit) #: sets the current MUnit self.listw_units.currentItemChanged.connect(self.set_unit) str = '' #: currently selected ``Channel`` self.channels: List[str] = [] #: list of ``Channel`` options available in current ``MUnit`` self.listw_channels: ListWidget = list_widgets[2] #: ui list of ``Channel`` options self.listw_channels.itemClicked.connect(self.set_channel) #: sets the current ``Channel`` self.listw_channels.currentItemChanged.connect(self.set_channel) self.listw_channels.itemDoubleClicked.connect(self._channel_clicked)
[docs] def set_file_path(self, path: str): """ set the path to the .mesc file :param path: path to the .mesc hdf5 file """ f = h5py.File(path, mode='r') # Check if "MSession_X" keys exist in the file has_session_key = any( k.startswith('MSession') for k in f.keys() ) if not has_session_key: raise TypeError( "The chosen file does not appear to be a valid " "`.mesc` file since it does not contain any " "'MSession_X' data group(s)." ) self.path = path self.file = f # just clear out everything self.session: str = '' self.sessions: List[str] = list(self.file.keys()) self._sort_list(self.sessions) self.listw_sessions.setItems(self.sessions) self.unit: str = '' self.units: List[str] = [] self.listw_units.clear() str = '' self.channels: List[str] = [] self.listw_units.clear() self.sig_hpath_changed.emit(self.get_hpath(dict))
[docs] def close_file(self): """ Close the h5py file handle that is currently open. """ if self.file is None: raise ValueError( 'No file is currently open' ) # close the hpy file handle self.file.close() # reset attributes to None self.file = None self.path = '' self.session: str = '' self.sessions: List[str] = [] self.listw_sessions.clear() self.unit: str = '' self.units: List[str] = [] self.listw_units.clear() str = '' self.channels: List[str] = [] self.listw_channels.clear() self.sig_hpath_changed.emit(self.get_hpath(dict))
[docs] def set_session(self, key: Union[str, QtWidgets.QListWidgetItem]): """ Set the MSession option :param key: a valid ``MSession`` :return: """ key = self._get_listw_text(key) if key is None: return if key not in self.sessions: raise KeyError(f"Session <{key}> not found in current file") self.session = key self.unit = '' self.units = list(self.file[self.session].keys()) self._sort_list(self.units) self.listw_units.setItems(self.units) = '' self.channels: List[str] = [] self.listw_channels.clear() self.sig_hpath_changed.emit(self.get_hpath(dict))
[docs] def set_unit(self, key: Union[str, QtWidgets.QListWidgetItem]): """ Set the MUnit option :param key: a valid ``MUnit`` :return: """ key = self._get_listw_text(key) if key is None: return if isinstance(key, QtWidgets.QListWidgetItem): key = key.text() if key not in self.units: raise KeyError(f"Unit <{key}> not found in current MSession") self.unit = key = '' self.channels = list(self.file[self.session][self.unit].keys()) self._sort_list(self.channels) self.listw_channels.setItems(self.channels) self.listw_channels.setCurrentRow(0) self.sig_hpath_changed.emit(self.get_hpath(dict))
[docs] def set_channel(self, key: Union[str, QtWidgets.QListWidgetItem]): """ Set a Channel or Curve option :param key: a valid ``Channel`` or ``Curve`` :return: """ key = self._get_listw_text(key) if key is None: return if key not in self.channels: raise KeyError(f"Channel <{key}> not found in current MUnit") = key self.sig_hpath_changed.emit(self.get_hpath(dict))
def _channel_clicked(self): if self.sig_channel_doubleclicked.emit(self.get_hpath(dict))
[docs] def get_hpath(self, astype: type) -> Union[str, list, dict]: """ get the current hdf path :param astype: one of `str`, `list`, or `dict` :return: the hdf path as the chosen data type """ path = [self.session, self.unit,] if astype is str: return '/'.join( filter(None, path) ) elif astype is list: return path elif astype is dict: return { 'session': self.session, 'unit': self.unit, 'channel': }
def _get_listw_text(self, item: [str, QtWidgets.QListWidgetItem]) -> str: if isinstance(item, QtWidgets.QListWidgetItem): return item.text() else: return item def _sort_list(self, l: list): l.sort( key=lambda name: int( regex_sub(r"[^0-9]*", '', name) ) )
[docs]class ModuleGUI(QtWidgets.QDockWidget): def __init__(self, parent, viewer_ref): # when a ModuleGUI() is instantiated the # Viewer Window passes the viewer reference (viewer_ref) # which can be used to interface with the viewer = ViewerUtils(viewer_ref) # this is used to interface with the viewer QtWidgets.QDockWidget.__init__(self, parent) self.ui = Ui_DockWidget() self.ui.setupUi(self) self.setWindowTitle('.mesc importer') self.ui.pushButton_open_file.clicked.connect(self.set_file) self.ui.pushButton_close_file.clicked.connect(self.close_file) self.ui.pushButton_import_image.clicked.connect(self.import_recording) # the list widgets for navigation list_widgets = [ self.ui.listWidget_session, self.ui.listWidget_unit, self.ui.listWidget_channel ] self.mesc_navigator = MEScNavigator(self, list_widgets) #: instance of ``MEScNavigator`` self.mesc_navigator.sig_hpath_changed.connect(self._set_comment_line) self.mesc_navigator.sig_hpath_changed.connect(self._enable_import_button) self.mesc_navigator.sig_channel_doubleclicked.connect( self._channel_doubleclicked ) self.plot_widgets = [] #: list of plot widgets
[docs] @present_exceptions( 'Could not load file', 'The following error occurred while trying to load hte .mesc file.' ) @use_open_file_dialog('Choose .mesc file', None, ['*.mesc']) def set_file(self, path: str, *args): """ Create an h5py file handle from the `.mesc` file at the given ``path``. ``*args`` are not used, its just there for compatibility with the decorator. :param path: path to the `.mes` file :type path: str :param args: not used """ self.mesc_navigator.set_file_path(path) # set the name of the current file in the GUI label self.ui.label_current_file_name.setText( os.path.basename(path) )
[docs] @present_exceptions( 'Could not close file', 'The following error occurred while trying to close the file handle.' ) def close_file(self, *args): """ Close the file handle :param args: ``*args`` not used, just there for compatibility with the decorator """ self.mesc_navigator.close_file() self.ui.label_current_file_name.clear()
def _enable_import_button(self, hpath: dict): if hpath['channel']: self.ui.pushButton_import_image.setEnabled(True) self.ui.pushButton_import_stim_map.setEnabled(True) else: self.ui.pushButton_import_image.setEnabled(False) self.ui.pushButton_import_stim_map.setEnabled(False) def _channel_doubleclicked(self, hpath: dict): if hpath['channel'].startswith('Channel'): self.import_recording() elif hpath['channel'].startswith('Curve'): f = self.mesc_navigator.file hpath = self.mesc_navigator.get_hpath(str) ys = f[hpath]['CurveDataYRawData'][()] if 'CurveDataXRawData' in f[hpath].keys(): xs = f[hpath]['CurveDataXRawData'][()] else: xs = np.arange(ys.size) pw = PlotWidget(parent=None) pw.plot(xs, ys, title=hpath) self.plot_widgets.append(pw) def _set_comment_line(self, hpath: dict): if hpath['unit']: f = self.mesc_navigator.file comment = f[hpath['session']][hpath['unit']].attrs['Comment'] comment = ascii_to_str(comment) self.ui.lineEdit_comment.setText(comment) else: self.ui.lineEdit_comment.clear()
[docs] @present_exceptions( 'Could not import recording', 'The following error occurred while trying to import the chosen recording' ) def import_recording(self, *args): """ Imports the chosen recording into the Viewer Work Environment based on the user selected hpath from the list widgets ``*args`` not used, just there for compatibility with the decorator """ if not return # Load the image sequence stored in this `MUnit_X` f = self.mesc_navigator.file # hdf file handle hpath = self.mesc_navigator.get_hpath(str) # hdf path img_seq = bitwise_not( # load & invert image array f[hpath][()] ) sess = self.mesc_navigator.get_hpath(dict)['session'] unit = self.mesc_navigator.get_hpath(dict)['unit'] # get the time for a single frame frame_time = \ f[sess][unit].attrs['ZAxisConversionConversionLinearScale'] + \ f[sess][unit].attrs['ZAxisConversionConversionLinearOffset'] z_units = ascii_to_str(f[sess][unit].attrs['ZAxisConversionUnitName']) if z_units != 'ms': raise TypeError(f"Z-axis units <{z_units}> not supported") # get the sampling rate fps = 1 / (frame_time / 1000) # for now just assuming the frame time are always in milliseconds # get the date of the recording date = datetime.fromtimestamp( f[sess][unit].attrs['MeasurementDatePosix'] ) # format the date into YYYYMMDD_HHMMSS date_str = date.strftime('%Y%m%d_%H%M%S') # create a minimal meta data dict that is required for the Viewer Work Environment. # the keys ``fps``, ``origin`` and ``date`` are mandatory meta = \ { 'fps': fps, 'origin': 'femtonics .mesc', 'date': date_str, } # Create an ``ImgData`` object, see the ImgData class under Viewer Core API for more information imgdata = ImgData(img_seq.T, meta) # Create a new Viewer Work Environment object using this ``ImgData`` object = ViewerWorkEnv(imgdata) # Update the GUI according to the new ViewerWorkEnv # set the "Current Image sequence" in the Viewer