#!/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 ..core.common import ViewerUtils
from .pytemplates.caiman_motion_correction_pytemplate import *
from ...common import get_window_manager
from ...pyqtgraphCore import LinearRegionItem
from uuid import UUID
from copy import deepcopy
from joblib import Parallel, delayed
import numpy as np
from psutil import cpu_count
import tifffile
from ...pyqtgraphCore.widgets.MatplotlibWidget import MatplotlibWidget
import os
from math import ceil
from itertools import product
from typing import *
import logging
logger = logging.getLogger()
[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.btnAddToBatchElastic.clicked.connect(self.add_to_batch_elas_corr)
self.ui.btnShowQuilt.clicked.connect(self.draw_quilt)
self.ui.sliderOverlaps.valueChanged.connect(self.draw_quilt)
self.ui.sliderStrides.valueChanged.connect(self.draw_quilt)
self.overlapsH = []
self.overlapsV = []
self.ncols_projection_plots = 3
self.cmap_projection_plots = 'gray'
self.projections_plot_widget = None
self.projections_plot_vmin_vmax_stds = 5
self.currrent_projections: List[np.ndarray] = None
self.ui.pushButtonViewProjections.clicked.connect(self.view_output_projections)
def draw_quilt(self):
if self.ui.btnShowQuilt.isChecked() is False:
self.remove_quilt()
return
if len(self.overlapsV) > 0:
for overlap in self.overlapsV:
self.vi.viewer.view.removeItem(overlap)
for overlap in self.overlapsH:
self.vi.viewer.view.removeItem(overlap)
self.overlapsV = []
self.overlapsH = []
w = int(self.vi.viewer.view.addedItems[0].width())
k = self.ui.sliderStrides.value()
h = int(self.vi.viewer.view.addedItems[0].height())
j = self.ui.sliderStrides.value()
val = int(self.ui.sliderOverlaps.value())
for i in range(1, int(w / k) + 1):
linreg = LinearRegionItem(values=[i * k, i * k + val], brush=(255, 255, 255, 80),
movable=False, bounds=[i * k, i * k + val])
self.overlapsV.append(linreg)
self.vi.viewer.view.addItem(linreg)
for i in range(1, int(h / j) + 1):
linreg = LinearRegionItem(values=[i * j, i * j + val], brush=(255, 255, 255, 80),
movable=False, bounds=[i * j, i * j + val],
orientation=LinearRegionItem.Horizontal)
self.overlapsH.append(linreg)
self.vi.viewer.view.addItem(linreg)
def remove_quilt(self):
for o in self.overlapsV:
self.vi.viewer.view.removeItem(o)
for o in self.overlapsH:
self.vi.viewer.view.removeItem(o)
self.overlapsH = []
self.overlapsV = []
[docs] def get_params(self, group_params: bool = False) -> dict:
"""
Get a dict of the set parameters
:return: parameters dict
:rtype: dict
"""
if self.ui.spinBoxGSig_filt.value() == 0:
gSig_filt = None
else:
gSig = self.ui.spinBoxGSig_filt.value()
gSig_filt = (gSig, gSig)
d = \
{
'output_bit_depth': self.ui.comboBoxOutputBitDepth.currentText(),
'template': None
}
mc_params = \
{
'max_shifts': (self.ui.spinboxX.value(), self.ui.spinboxY.value()),
'niter_rig': self.ui.spinboxIterRigid.value(),
'max_deviation_rigid': self.ui.spinboxMaxDev.value(),
'strides': (self.ui.sliderStrides.value(), self.ui.sliderStrides.value()),
'overlaps': (self.ui.sliderOverlaps.value(), self.ui.sliderOverlaps.value()),
'upsample_factor_grid': self.ui.spinboxUpsample.value(),
'gSig_filt': gSig_filt
}
# Update the dict with any user entered kwargs
if self.ui.groupBox_motion_correction_kwargs.isChecked():
_kwargs = self.ui.plainTextEdit_mc_kwargs.toPlainText()
mc_params.update(eval(f"dict({_kwargs})"))
if self.vi.viewer.workEnv.imgdata.ndim == 4:
is_3d = True
else:
is_3d = False
d['is_3d'] = is_3d
if group_params:
d.update({'mc_kwargs': mc_params})
else:
d.update({**mc_params})
return d
[docs] def add_to_batch_elas_corr(self):
"""
Add a batch item with the currently set parameters and the current work environment.
"""
name = self.ui.lineEditNameElastic.text()
self.vi.viewer.status_bar_label.showMessage(
'Please wait, adding CaImAn motion correction: ' + name + ' to batch...')
self.add_to_batch()
self.vi.viewer.status_bar_label.showMessage('Done adding CaImAn motion correction: ' + name + ' to batch!')
self.ui.lineEditNameElastic.clear()
def add_to_batch(self, params: dict = None) -> UUID:
if params is None:
input_params = self.get_params(group_params=True)
item_name = self.ui.lineEditNameElastic.text()
input_params['item_name'] = item_name
else:
# check that params dict is formatted properly
required_keys = ['item_name', 'mc_kwargs', 'output_bit_depth']
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.')
input_params = deepcopy(params)
item_name = input_params['item_name']
input_workEnv = self.vi.viewer.workEnv
batch_manager = get_window_manager().get_batch_manager()
u = batch_manager.add_item(module='caiman_motion_correction',
name=item_name,
input_workEnv=input_workEnv,
input_params=input_params,
info=input_params
)
return u
@staticmethod
def _get_projection(proj_type: str, batch_path: str, item_uuid: UUID):
tiff_path = os.path.join(batch_path, f'{item_uuid}_mc.tiff')
tif = tifffile.TiffFile(tiff_path, is_nih=True)
seq = tif.asarray(maxworkers=cpu_count())
func = getattr(np, f"nan{proj_type}")
return func(seq, axis=0)
def view_output_projections(self):
batch_manager = get_window_manager().get_batch_manager()
batch_path = batch_manager.batch_path
items = batch_manager.get_selected_items() # get a list of indices and UUIDs for the selected items
self._projection_item_indices = items[0]
item_uuids = items[1]
if len(self._projection_item_indices) > 3:
if QtWidgets.QMessageBox.question(
self, 'Many items selected',
f"You have selected < {len(self._projection_item_indices)} > items, "
f"it may take a while to calculate these projections.\n"
f"Do you still want to continue?",
QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.Yes
) == QtWidgets.QMessageBox.No:
return
proj = self.ui.comboBoxProjectionsOption.currentText()
logger.info("Calculating projections, please wait...")
self.currrent_projections = Parallel(n_jobs=cpu_count(), verbose=5)(
delayed(ModuleGUI._get_projection)(proj, batch_path, item_uuid) for item_uuid in item_uuids
)
self.nrows_projection_plots = ceil(len(self._projection_item_indices) / self.ncols_projection_plots)
self.plot_output_projections()
def plot_output_projections(self):
if self.currrent_projections is None:
raise AttributeError("Projections not calculated")
logger.info("Plotting projections")
if self.projections_plot_widget is None:
self.projections_plot_widget = MatplotlibWidget()
else:
self.projections_plot_widget.fig.clear()
self.projections_plot_widget.axs = self.projections_plot_widget.fig.subplots(self.nrows_projection_plots, self.ncols_projection_plots)
for i, axes_ix in enumerate(
product(range(self.nrows_projection_plots), range(self.ncols_projection_plots))
):
if not i < len(self._projection_item_indices):
break
index = self._projection_item_indices[i]
projection = self.currrent_projections[i]
proj_mean = np.nanmean(projection)
proj_std = np.nanstd(projection)
z = self.projections_plot_vmin_vmax_stds * proj_std
vmin = max(proj_mean - z, np.nanmin(projection))
vmax = min(proj_mean + z, np.nanmax(projection))
self.projections_plot_widget.axs[axes_ix].imshow(
projection,
cmap=self.cmap_projection_plots,
vmin=vmin,
vmax=vmax
)
self.projections_plot_widget.axs[axes_ix].set_title(index)
self.projections_plot_widget.axs[axes_ix].set_title(index)
self.projections_plot_widget.fig.tight_layout()
self.projections_plot_widget.draw()
self.projections_plot_widget.show()