#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on April 23 2018
@author: kushal
Chatzigeorgiou Group
Sars International Centre for Marine Molecular Biology
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
"""
from ..core.common import ViewerUtils
from .pytemplates.cnmfe_pytemplate import *
import json
from ...common import get_window_manager
from ...common.qdialogs import *
from uuid import UUID
from copy import deepcopy
[docs]class ModuleGUI(QtWidgets.QDockWidget):
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.btnAddToBatchCorrPNR.clicked.connect(lambda: self.add_to_batch_corr_pnr())
self.ui.btnAddToBatchCNMFE.clicked.connect(lambda: self.add_to_batch_cnmfe())
[docs] @present_exceptions()
def get_params(self, item_type: str, group_params: bool = False) -> dict:
"""
Get a dict of the set parameters.
If the work environment was loaded from a motion correction batch item it put the bord_px in the dict.
Doesn't use any arguments
:param item_type: one of `corr_pnr` or `cnmfe`
"""
if self.vi.viewer.workEnv.imgdata.meta['fps'] == 0:
raise KeyError('No framerate for current image sequence!',
'You must set a framerate for the current image sequence. '
'You can set it manually in the console like this:\nget_meta()["fps"] = <framerate>')
# Get bord_px param if motion correction was performed
history_trace = self.vi.viewer.workEnv.history_trace
try:
bord_px = next(d for ix, d in enumerate(history_trace) if 'caiman_motion_correction' in d)['caiman_motion_correction']['bord_px']
except StopIteration:
bord_px = 0
deconv = self.ui.comboBoxDeconv.currentText()
if deconv == 'SKIP':
method_deconvolution = None
deconv_flag = False
else:
deconv_flag = True
method_deconvolution = deconv
gSig = self.ui.spinBoxGSig.value()
# Correlation-PNR param
corr_pnr_kwargs = \
{
'gSig': gSig
}
kval = self.ui.spinBoxK.value()
if kval == 0:
kval = None
# CNMFE kwargs
cnmfe_kwargs = \
{
'gSig': (gSig, gSig),
'gSiz': (4 * gSig + 1, 4 * gSig + 1),
'border_pix': bord_px,
'rf': self.ui.spinBoxRf.value(),
'stride': self.ui.spinBoxOverlap.value(),
'gnb': self.ui.spinBoxGnb.value(),
'nb_patch': self.ui.spinBoxNb_patch.value(),
'K': kval,
'min_corr': self.ui.doubleSpinBoxMinCorr.value(),
'min_pnr': self.ui.spinBoxMinPNR.value(),
'deconv_flag': deconv_flag,
'method_deconvolution': method_deconvolution,
'Ain': self.ui.lineEditAin.text().replace(' ', '').strip('\n'),
'p': self.ui.spinBox_p.value(),
'merge_thresh': self.ui.doubleSpinBoxMergeThresh.value(),
'ssub': self.ui.spinBox_ssub.value(),
'tsub': self.ui.spinBox_tsub.value(),
'low_rank_background': self.ui.checkBox_low_rank_background.isChecked(),
'ring_size_factor': self.ui.doubleSpinBox_ring_size_factor.value(),
'update_background_components': True,
'del_duplicates': True
}
# Any additional CNMFE kwargs set in the text entry
if self.ui.groupBox_cnmf_kwargs.isChecked():
try:
_kwargs = self.ui.plainTextEdit_cnmf_kwargs.toPlainText()
cnmfe_kwargs_add = eval(f"dict({_kwargs})")
cnmfe_kwargs.update(cnmfe_kwargs_add)
except:
raise ValueError("CNMFE kwargs not formatted properly.")
# kwargs for component evaluation
eval_kwargs = \
{
'fr': self.vi.viewer.workEnv.imgdata.meta['fps'],
'min_SNR': self.ui.spinBoxMinSNR.value(),
'rval_thr': self.ui.doubleSpinBoxRValuesMin.value(),
'decay_time': self.ui.doubleSpinBoxDecayTime.value(),
}
# Any additional eval kwargs set in the text entry
if self.ui.groupBox_eval_kwargs.isChecked():
try:
_kwargs = self.ui.plainTextEdit_eval_kwargs.toPlainText()
eval_kwargs_add = eval(f"dict({_kwargs})")
eval_kwargs.update(eval_kwargs_add)
except:
raise ValueError("Evaluation kwargs not formatted properly.")
# Output either the dict for corr-pnr or CNMFE
if item_type == 'corr_pnr':
item_name = self.ui.lineEdCorrPNRName.text()
d = \
{
'item_name': item_name,
'do_cnmfe': False,
'do_corr_pnr': True,
'border_pix': bord_px
}
if group_params:
d.update({'corr_pnr_kwargs': corr_pnr_kwargs})
else:
d.update({**corr_pnr_kwargs})
elif item_type == 'cnmfe':
item_name = self.ui.lineEdName.text()
d = \
{
'item_name': item_name,
'do_cnmfe': True,
'do_corr_pnr': False,
'border_pix': bord_px
}
if group_params:
d.update(
{
'cnmfe_kwargs': cnmfe_kwargs,
'eval_kwargs': eval_kwargs,
}
)
else:
d.update(
{
**cnmfe_kwargs,
**eval_kwargs
}
)
else:
raise ValueError("Must specify argument `item_type` as either 'corr_pnr' or 'cnmfe'")
d['keep_memmap'] = self.ui.checkBoxKeepMemmap.isChecked()
return d
[docs] def add_to_batch_corr_pnr(self, params: dict = None) -> UUID:
"""
Add a Corr PNR batch item with the currently set parameters and the current work environment.
"""
if self.vi.viewer.workEnv.isEmpty:
QtWidgets.QMessageBox.warning(self, 'Empty work environment', 'The work environment is empty, '
'nothing to add to batch')
return
input_workEnv = self.vi.viewer.workEnv
if params is None:
d = self.get_params('corr_pnr', group_params=True)
else:
# Check that user passed dict is formatted correctly
required_keys = ['item_name', 'do_cnmfe', 'do_corr_pnr', 'border_pix', 'corr_pnr_kwargs']
if any([k not in params.keys() for k in required_keys]):
raise ValueError(f'Must pass a params dict with the following keys:\n'
f'{required_keys}\n'
f'Please see the docs for more information.')
d = deepcopy(params)
batch_manager = get_window_manager().get_batch_manager()
name = d['item_name']
self.vi.viewer.status_bar_label.showMessage('Please wait, adding Corr PNR: ' + name + ' to batch...')
u = batch_manager.add_item(module='CNMFE',
name=name,
input_workEnv=input_workEnv,
input_params=d,
info=d
)
self.vi.viewer.status_bar_label.showMessage('Done adding Corr PNR: ' + name + ' to batch!')
self.clear_line_edits()
return u
[docs] def add_to_batch_cnmfe(self, params: dict = None) -> UUID:
"""
Add a CNMFE batch item with the currently set parameters and the current work environment.
"""
if self.vi.viewer.workEnv.isEmpty:
QtWidgets.QMessageBox.warning(self, 'Empty work environment', 'The work environment is empty, '
'nothing to add to batch')
return
input_workEnv = self.vi.viewer.workEnv
if params is None:
d = self.get_params('cnmfe', group_params=True)
else:
# Check that user passed dict is formatted correctly
required_keys = ['item_name', 'do_cnmfe', 'do_corr_pnr', 'border_pix', 'cnmfe_kwargs', 'eval_kwargs']
if any([k not in params.keys() for k in required_keys]):
raise ValueError(f'Must pass a params dict with the following keys:\n'
f'{required_keys}\n'
f'Please see the docs for more information.')
d = deepcopy(params)
name = d['item_name']
self.vi.viewer.status_bar_label.showMessage('Please wait, adding CNMFE: ' + name + ' to batch...')
batch_manager = get_window_manager().get_batch_manager()
u = batch_manager.add_item(module='CNMFE',
name=name,
input_workEnv=input_workEnv,
input_params=d,
info=d
)
if u is None:
self.vi.viewer.status_bar_label.clearMessage()
return
self.vi.viewer.status_bar_label.showMessage('Done adding CNMFE: ' + name + ' to batch!')
self.clear_line_edits()
return u
def clear_line_edits(self):
self.ui.lineEdCorrPNRName.clear()
self.ui.lineEdName.clear()
self.ui.lineEditAin.clear()