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Commit bf7df136 authored by Yan's avatar Yan
Browse files

Unite spectrum variables and objects into one class

parent 14dcd27b
Hide whitespace changes
Inline Side-by-side
prasopes/__main__.py
View file @ bf7df136
......@@ -49,16 +49,44 @@ class QStatusBarLogger(logging.Handler):
self.trigger.signal.emit()
def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
update, settings, loadthread, filename=None):
class AugFigureCanvas(FigureCanvas):
#TODO: move the widget into graphtools when I'm done
def __init__(self):
self.figure = Figure(figsize=(5, 4), dpi=100, facecolor="None",
constrained_layout=True)
super().__init__(self.figure)
self.ds = []
self.ms = dict(annotation=[], name="Spectrum", xlabel="m/z",
ylabel="ion count", xtics=20, predict=None,
params=[], headers=[], texts=[])
self.chrom = dict(x=[0], y=[0], t_start=None, t_end=None, machtype=None,
name="Chromatogram", xlabel="time(min)",
ylabel="total ion count", timesarg=[])
self.filename = None
self.drlcache = [None, None]
grid = self.figure.add_gridspec(2, 1)
self.chromplot = self.figure.add_subplot(grid[0,0], facecolor=(1, 1, 1, 0.8))
self.spectplot = self.figure.add_subplot(grid[1,0], facecolor=(1, 1, 1, 0.8))
self.setStyleSheet("background-color:transparent;")
self.setAutoFillBackground(False)
self.paramstable = dt.table(["","name","value"], 100)
gt.pan_factory(self.chromplot)
gt.zoom_factory(self.chromplot, 1.15)
gt.pan_factory(self.spectplot, self.ms)
gt.zoom_factory(self.spectplot, 1.15, self.ms)
gt.textedit_factory(self.spectplot, self.ms)
self.mass_selector = gt.AugSpanSelector(self.spectplot, self.ms)
#TODO: rewrite timeSelector to better shape when I'm done
self.time_selector = SpanSelector(self.chromplot, lambda x_min, x_max:
gt.pick_times(x_min, x_max, self.spectplot, self.ds, self.chromplot, self.ms, self.chrom, self.paramstable), 'horizontal', useblit=True, rectprops=dict(
alpha=0.15, facecolor='purple'), button=3)
def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
"""populates dataset and plots it"""
directory=settings.value("open_folder")
if fn[0] is not None:
directory=fn[0]
if filename == None:
filename = QtWidgets.QFileDialog.getOpenFileName(
caption="Open spectrum",
directory=directory,
directory = augCanvas.filename or settings.value("open_folder")
filename = filename or QtWidgets.QFileDialog.getOpenFileName(
caption="Open spectrum", directory=directory,
filter="Finnigan RAW files (*.raw, *.RAW)")[0]
if filename is not '' and os.path.isfile(filename)\
and not os.path.isdir(filename):
......@@ -67,8 +95,10 @@ def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
def runfnc():
try:
[i.clear() for i in (
d_set, chrom_s['timesarg'], ms_s['params'],ms_s['headers'])]
[d_set.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2]))
augCanvas.ds, augCanvas.chrom['timesarg'],
augCanvas.ms['params'],augCanvas.ms['headers'])]
[augCanvas.ds.append(dict(
chrom_dat=i[0], masses=i[1], matrix=i[2]))
for i in load_raw(filename, settings.value("tmp_location"))]
except rawprasslib.ParsingException as pex:
errormsg.append("Opening of the file has failed!")
......@@ -80,18 +110,23 @@ def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
return
if autoparams == True:
try:
ms_s['params'], rawheaders, chrom_s['machtype'] = load_params(filename)
segments = [len(subset['chrom_dat'][0]) for subset in d_set]
indicies = [sum(segments[:i+1]) for i in range(len(segments))]
ms_s['headers'] = np.split(rawheaders, indicies)[:-1]
(augCanvas.ms['params'], rawheaders
, augCanvas.chrom['machtype']) = load_params(filename)
segments = [len(subset['chrom_dat'][0])
for subset in augCanvas.ds]
indicies = [sum(segments[:i+1])
for i in range(len(segments))]
augCanvas.ms['headers'] = np.split(
rawheaders, indicies)[:-1]
except Exception as pex:
errormsg.append("File is incompatible with the rawautoparams,")
errormsg.append(
"File is incompatible with the rawautoparams,")
errormsg.append(
"no parameters loaded!\n\n"
"Error message:\n{}".format(pex.args[0]))
error.signal.emit()
gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
fn[0] = filename
gt.populate(augCanvas)
augCanvas.filename = filename
parent.setWindowTitle("Prasopes - {}".format(
os.path.basename(filename)))
update.signal.emit()
......@@ -175,17 +210,17 @@ def oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom, config,
update_spectrum(chromatogram, spectrum, ds, ms, filename, chrom, config)
def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config):
def key_pressed(event, augCanvas, config):
if event.key() == QtCore.Qt.Key_F5:
update_spectrum(chrom, spect, ds, ms_ds, fn, chrom_ds, config)
update_spectrum(augCanvas, config)
if event.key() == QtCore.Qt.Key_C:
if event.modifiers().__int__() == QtCore.Qt.ControlModifier:
imgt.clip_spect_img(ms_ds, spect)
imgt.clip_spect_img(augCanvas)
if event.modifiers().__int__() == QtCore.Qt.ControlModifier+\
QtCore.Qt.ShiftModifier:
dt.clip_spectstr(spect, chrom_ds, fn)
dt.clip_spectstr(augCanvas)
if event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):
gt.shift_times(event, spect, chrom, ds, ms_ds, chrom_ds)
gt.shift_times(event, augCanvas)
def about(parent):
......@@ -200,15 +235,7 @@ def main():
app = QtWidgets.QApplication(sys.argv)
loadthread = QtCore.QThread()
ds = []
ms = dict(annotation=[], name="Spectrum", xlabel="m/z",
ylabel="ion count", xtics=20, predict=None,
params=[], headers=[], texts=[])
chrom = dict(x=[0], y=[0], t_start=None, t_end=None, machtype=None,
name="Chromatogram", xlabel="time(min)",
ylabel="total ion count", timesarg=[])
filename = [None]
drlcache = [None, None]
augCanvas = AugFigureCanvas()
update = update_signal()
config = cf.settings()
......@@ -235,60 +262,35 @@ def main():
params_logger.addHandler(barHandler)
barHandler.setLevel("DEBUG")
paramstable = dt.table(["","name","value"], 100)
paramstable.horizontalHeader().setSectionResizeMode(
0, QtWidgets.QHeaderView.ResizeToContents)
graph = Figure(figsize=(5, 4), dpi=100, facecolor="None", constrained_layout=True)
grid = graph.add_gridspec(2, 1)
chromatogram = graph.add_subplot(grid[0,0], facecolor=(1, 1, 1, 0.8))
spectrum = graph.add_subplot(grid[1,0], facecolor=(1, 1, 1, 0.8))
mpl_canvas = FigureCanvas(graph)
mpl_canvas.setStyleSheet("background-color:transparent;")
mpl_canvas.setAutoFillBackground(False)
gt.pan_factory(chromatogram)
gt.zoom_factory(chromatogram, 1.15)
gt.pan_factory(spectrum, ms)
gt.zoom_factory(spectrum, 1.15, ms)
gt.textedit_factory(spectrum, ms)
mass_selector = gt.AugSpanSelector(spectrum, ms)
time_selector = SpanSelector(chromatogram, lambda x_min, x_max:
gt.pick_times( x_min, x_max, spectrum, ds, chromatogram, ms, chrom,
paramstable), 'horizontal', useblit=True, rectprops=dict(
alpha=0.15, facecolor='purple'), button=3)
main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")
if QtGui.QIcon.themeName() is "":
QtGui.QIcon.setThemeName("TangoMFK")
lfvars = (main_window, chromatogram, spectrum, ds, ms, filename, chrom,
update, config, loadthread)
consoledock = docks.consoleDockWidget(
locals(), "&Console", "view/consolevisible")
treedock = docks.treeDockWidget(
update, "&File browser", "view/filebrowservisible", load_file, lfvars)
"&File browser", "view/filebrowservisible", update, load_file, main_window,
augCanvas, config, loadthread)
paramsdock = docks.augDock("Acquisition parameters", "&Acq parameters",
"view/acqparvisible")
update.signal.connect(lambda: gt.update_paramstable(paramstable, ms, chrom))
paramsdock.setWidget(paramstable)
update.signal.connect(lambda: gt.update_paramstable(augCanvas))
paramsdock.setWidget(augCanvas.paramstable)
openact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
"document-open"), "&Open...", None)
openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
openact.triggered.connect(lambda: load_file(
main_window, chromatogram, spectrum, ds, ms, filename, chrom,
update, config, loadthread))
main_window, augCanvas, update, config, loadthread))
exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
"document-save-as"), "&Export...", None)
exportact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_E)
exportact.triggered.connect(lambda: ft.export_dial(
spectrum, chrom, filename, main_window))
augCanvas, main_window))
printact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
"document-print"), "&Print", None)
printact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_P)
printact.triggered.connect(lambda: print_graph(
ds, ms, chrom, spectrum, filename, paramstable))
printact.triggered.connect(lambda: print_graph(augCanvas))
settingsact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
"preferences-system"), "&Settings...", None)
settingsact.triggered.connect(lambda: cf.dial(main_window))
......@@ -300,12 +302,12 @@ def main():
"applications-utilities"), "&TSQ zce...", None)
zceact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_T)
zceact.triggered.connect(lambda: zce.dialog(
main_window, ds, filename, update))
main_window, augCanvas, update))
drlact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
"applications-utilities"), "&DRL...", None)
drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
drlact.triggered.connect(lambda: drl.main_window(
main_window, ds, filename, drlcache, update))
main_window, augCanvas, update))
aboutact = QtWidgets.QAction("&About Prasopes", None)
aboutact.triggered.connect(lambda: about(main_window))
autozoomy = QtWidgets.QAction(QtGui.QIcon.fromTheme(
......@@ -313,23 +315,22 @@ def main():
checked=config.value("view/autozoomy", type=bool))
autozoomy.triggered.connect(lambda: config.setValue(
"view/autozoomy", autozoomy.isChecked()))
autozoomy.triggered.connect(lambda: gt.autozoomy(spectrum))
autozoomy.triggered.connect(lambda: gt.autozoomy(augCanvas.spectrum))
intensitiesact = QtWidgets.QAction("&Show intensities", None,
checkable=True, checked=config.value("view/intensities",
type=bool))
intensitiesact.triggered.connect(lambda: config.setValue(
"view/intensities", intensitiesact.isChecked()))
intensitiesact.triggered.connect(lambda: gt.ann_spec(spectrum, ms))
intensitiesact.triggered.connect(lambda: spectrum.figure.canvas.draw())
intensitiesact.triggered.connect(lambda: gt.ann_spec(augCanvas))
intensitiesact.triggered.connect(lambda: augCanvas.draw())
oddevenact = QtWidgets.QAction("&Odd / even", None, checkable=True,
checked=config.value("view/oddeven", type=bool))
oddevenact.triggered.connect(lambda:
oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom,
config, oddevenact))
oddeven_changed(augCanvas, config, oddevenact))
predictform = QtWidgets.QLineEdit(maximumWidth=150)
predictform.editingFinished.connect(lambda: predictmz(
predictform, chromatogram, spectrum, ds, ms, chrom))
predictform, augCanvas))
file_menu = QtWidgets.QMenu('&File', main_window)
main_window.menuBar().addMenu(file_menu)
......@@ -356,8 +357,7 @@ def main():
main_window.menuBar().addMenu(help_menu)
help_menu.addAction(aboutact)
main_window.setCentralWidget(mpl_canvas)
main_window.setCentralWidget(augCanvas)
toolBar = QtWidgets.QToolBar(main_window)
toolBar.setAllowedAreas(QtCore.Qt.TopToolBarArea)
......@@ -378,11 +378,10 @@ def main():
main_window.dragEnterEvent = lambda event: drag_entered(event)
main_window.dropEvent = lambda event: dropped(
event, main_window, chromatogram, spectrum, ds, ms, filename,
chrom, update, config)
event, main_window, augCanvas, update, config)
main_window.setAcceptDrops(True)
main_window.keyPressEvent = lambda event: key_pressed(event, chromatogram,
spectrum, ds, ms, filename, chrom, config)
main_window.keyPressEvent = lambda event: key_pressed(
event, augCanvas, config)
main_window.addToolBar(QtCore.Qt.TopToolBarArea, toolBar)
main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)
......@@ -393,12 +392,11 @@ def main():
main_window.setFocus()
if len(sys.argv) == 2:
load_file(main_window, chromatogram, spectrum, ds, ms,
filename, chrom, update, config, loadthread,
load_file(main_window, augCanvas, update, config, loadthread,
filename=sys.argv[1])
else:
gt.pop_plot(0, 0, spectrum, ms)
gt.pop_plot(0, 0, chromatogram, chrom)
gt.pop_plot(0, 0, augCanvas.spectplot, augCanvas.ms)
gt.pop_plot(0, 0, augCanvas.chromplot, augCanvas.chrom)
main_window.show()
sys.exit(app.exec_())
......
prasopes/docks.py
View file @ bf7df136
......@@ -3,7 +3,7 @@
from PyQt5 import QtWidgets
from code import InteractiveConsole
from io import StringIO
import os
from os import path
import contextlib
import numpy as np
import prasopes.config as cf
......@@ -57,7 +57,8 @@ def consoleDockWidget(localvars, actionname, cfval):
return dock
def treeDockWidget(update, actionname, cfval, load_file, lfvars):
def treeDockWidget(actionname, cfval, update, loadfnc, parent,
augCanvas, config, loadthread):
config = cf.settings()
fileModel = QtWidgets.QFileSystemModel()
fileModel.setRootPath('')
......@@ -70,18 +71,18 @@ def treeDockWidget(update, actionname, cfval, load_file, lfvars):
dirview.setModel(fileModel)
dock = augDock("Folder View", actionname, cfval)
[dock.layout.addWidget(i) for i in (treeview, dirview)]
filename = lfvars[5]
def scrolltoonce():
fileModel.layoutChanged.disconnect(scrolltoonce)
treeview.scrollTo(fileModel.index(config.value("open_folder")), 1)
fileModel.directoryLoaded.connect(
lambda: treeview.resizeColumnToContents(0))
update.signal.connect(lambda: treeview.setCurrentIndex(fileModel.index(
filename[0])))
augCanvas.filename)))
update.signal.connect(lambda: dirview.setRootIndex(fileModel.index(
os.path.dirname(os.path.realpath(filename[0])))))
path.dirname(path.realpath(augCanvas.filename)))))
fileModel.layoutChanged.connect(scrolltoonce)
clickload = lambda index: load_file(*lfvars, filename=fileModel.filePath(index))
clickload = lambda index: loadfnc(parent, augCanvas, update, config,
loadthread, filename=fileModel.filePath(index))
for i in [treeview.doubleClicked, dirview.doubleClicked, dirview.clicked]:
i.connect(clickload)
return dock
prasopes/drltools.py
View file @ bf7df136
......@@ -620,8 +620,11 @@ def select_all_btn_up(ds, drls, drlspectrum, state=None):
drls['checkAll'].blockSignals(False)
def main_window(parent, ds, filename, cache, update_signal):
def main_window(parent, augCanvas, update_signal):
"""constructs a dialog window"""
ds = augCanvas.ds
filename = augCanvas.filename
cache = augCanvas.drlcache
def onclose(widget, event, buffer, drls, canvas, update_fnc, update_ptrows):
buffer[0], buffer[1] = drls, canvas
update_signal.signal.disconnect(update_fnc)
......
prasopes/graphtools.py
View file @ bf7df136
......@@ -20,7 +20,7 @@ ann_bbox = dict(boxstyle="round", fc="w", ec="0.5", alpha=0.5)
class AugSpanSelector(SpanSelector):
def __init__(self, ax, data):
SpanSelector.__init__(self, ax, onselect=lambda x,y: None,
super().__init__(ax, onselect=lambda x,y: None,
direction='horizontal', minspan=0.01, useblit=True,
rectprops=dict(alpha=0.15, facecolor='purple'),
onmove_callback=None, span_stays=False, button=3)
......@@ -36,14 +36,14 @@ class AugSpanSelector(SpanSelector):
self.direction = 'horizontal'
self.onselect = self.pick_masses
self.new_axes(self.ax)
SpanSelector._press(self, event)
super()._press(event)
def _release(self, event):
"""on button release event"""
if self.pressv is None:
return
elif self.direction == 'horizontal':
SpanSelector._release(self, event)
super()._release(event)
else:
self.rect.set_visible(False)
self.canvas.draw_idle()
......@@ -58,7 +58,7 @@ class AugSpanSelector(SpanSelector):
def _set_span_xy(self, event):
"""Setting the span coordinates override"""
if self.direction == 'horizontal':
SpanSelector._set_span_xy(self, event)
super()._set_span_xy(event)
else:
x,y = self._get_data(event)
if y is None:
......@@ -399,32 +399,30 @@ def legendize(rawlegend, chrom_data):
return strtext
def populate(mpl_chromatogram, mpl_spectrum, data_set,
ms_data, chrom_data):
def populate(augCanvas):
"""populate the GUI plots with desired dataset"""
if np.array_equal(data_set, []):
if np.array_equal(augCanvas.ds, []):
return
ms_data['annotation'].clear()
mpl_spectrum.clear()
mpl_chromatogram.clear()
[i.clear() for i in (augCanvas.ms['annotation'],
augCanvas.chromplot, augCanvas.spectplot)]
if ms_data['predict'] != None:
maxm = np.argmax(ms_data['predict'][1]) + ms_data['predict'][0]
if augCanvas.ms['predict'] != None:
predict = augCanvas.ms['predict']
maxm = np.argmax(predict[1]) + predict[0]
maxseek = dt.argsubselect(linex, maxm-.5, maxm+.5)
maxpos = maxseek[np.argmax(liney[maxseek])]
crudeints = ms_data['predict'][1] * ms_data['y'][maxpos]
crudemasses = (np.arange(len(ms_data['predict'][1])) +
linex[maxpos])
crudeints = predict[1] * ms_data['y'][maxpos]
crudemasses = (np.arange(len(predict[1])) + linex[maxpos])
pmasses, pints = [], []
[pmasses.extend([np.nan,i,i]) for i in crudemasses]
[pints.extend([np.nan,0,i]) for i in crudeints]
mpl_spectrum.plot(pmasses,pints, linewidth=1)
augCanvas.spectplot.plot(pmasses, pints, linewidth=1)
chrom_data['t_start'] = data_set[0]['chrom_dat'][0, 0]
chrom_data['t_end'] = data_set[-1]['chrom_dat'][0, -1]
for i,subset in enumerate(data_set):
if len(ms_data['headers']) == len(data_set):
legend = legendize(ms_data['headers'][i], chrom_data)
augCanvas.chrom['t_start'] = augCanvas.ds[0]['chrom_dat'][0, 0]
augCanvas.chrom['t_end'] = augCanvas.ds[-1]['chrom_dat'][0, -1]
for i,subset in enumerate(augCanvas.ds):
if len(augCanvas.ms['headers']) == len(augCanvas.ds):
legend = legendize(augCanvas.ms['headers'][i], augCanvas.chrom)
else:
legend = None
if cf.settings().value("view/oddeven", type=bool):
......@@ -433,17 +431,20 @@ def populate(mpl_chromatogram, mpl_spectrum, data_set,
msy = np.mean(subset['matrix'][j::2], axis=0)
chromx = subset['chrom_dat'][0, :][j::2]
chromy = subset['chrom_dat'][1, :][j::2]
pop_plot(msx, msy, mpl_spectrum, ms_data, i*2+j, legend)
pop_plot(chromx, chromy, mpl_chromatogram, chrom_data, i*2+j, legend)
pop_plot(msx, msy, augCanvas.spectplot, augCanvas.ms,
i*2+j, legend)
pop_plot(chromx, chromy, augCanvas.chromplot,
augCanvas.chrom, i*2+j, legend)
else:
msx = subset['masses']
msy = np.mean(subset['matrix'], axis=0)
chromx = subset['chrom_dat'][0, :]
chromy = subset['chrom_dat'][1, :]
pop_plot(msx, msy, mpl_spectrum, ms_data, i, legend)
pop_plot(chromx, chromy, mpl_chromatogram, chrom_data, i, legend)
for ax in (mpl_spectrum, mpl_chromatogram):
if not ms_data['headers'] == []:
pop_plot(msx, msy, augCanvas.spectplot, augCanvas.ms, i, legend)
pop_plot(chromx, chromy, augCanvas.chromplot, augCanvas.chrom,
i, legend)
for ax in (augCanvas.spectplot, augCanvas.chromplot):
if not augCanvas.ms['headers'] == []:
ax.legend(loc=2)
ax.get_legend().set_in_layout(False)
ax.autoscale(True)
......@@ -452,18 +453,19 @@ def populate(mpl_chromatogram, mpl_spectrum, data_set,
return
def update_paramstable(table, ms, chrom):
if len(ms['params']) == 0:
table.setRowCount(0)
def update_paramstable(augCanvas):
if len(augCanvas.ms['params']) == 0:
augCanvas.paramstable.setRowCount(0)
return
table.setRowCount(len(ms['params'][0]))
for row, paramname in enumerate(ms['params'][0]):
[table.setItem(row,col, QtWidgets.QTableWidgetItem())
augCanvas.paramstable.setRowCount(len(augCanvas.ms['params'][0]))
for row, paramname in enumerate(augCanvas.ms['params'][0]):
[augCanvas.paramstable.setItem(row,col, QtWidgets.QTableWidgetItem())
for col in range(1,3)]
table.setCellWidget(row,0,QtWidgets.QCheckBox())
table.item(row,1).setText(paramname)
vals = [param[row] for param in ms['params'][1]
if (param[0] >= chrom['t_start'] and param[0] <= chrom['t_end'])]
augCanvas.paramstable.setCellWidget(row,0,QtWidgets.QCheckBox())
augCanvas.paramstable.item(row,1).setText(paramname)
vals = [param[row] for param in augCanvas.ms['params'][1]
if (param[0] >= augCanvas.chrom['t_start'] and
param[0] <= augCanvas.chrom['t_end'])]
if len(vals) == 0:
text = ""
elif all([type(val) in [np.float32, np.float64] for val in vals]):
......@@ -474,4 +476,4 @@ def update_paramstable(table, ms, chrom):
else:
values = [str(i) for i in np.unique(np.array(vals), axis=0)]
text = " or ".join(values)
table.item(row,2).setText(text)
augCanvas.paramstable.item(row,2).setText(text)
prasopes/zcetools.py
View file @ bf7df136
......@@ -18,7 +18,7 @@ logger = logging.getLogger('zceLogger')
def pop_dial(zcespec, gradspect, data_set, coff_d, grad_d,
textfield, fn, parent):
logger.debug("populating ZCE dialog")
if fn[0] is None:
if fn is None:
QtWidgets.QMessageBox.warning(
parent, "ZCE calculation",
"No spectrum opened, nothing to display")
......@@ -67,7 +67,7 @@ def pop_dial(zcespec, gradspect, data_set, coff_d, grad_d,
def exp_zce(zce_spec, zcegrad_spec, fn, parent):
"""export the ZCE graph into the .dat file format"""
if fn[0] is None:
if fn is None:
QtWidgets.QMessageBox.warning(
parent, "Export ZCE spectrum",
"Nothing to export, cancelling request")
......@@ -79,7 +79,7 @@ def exp_zce(zce_spec, zcegrad_spec, fn, parent):
expf.write("mass ion_count ion_count_gradient fwhm_x fwhm_y\n"
"m/z\n"
"{} zce={} fwhm={} hmcenter={}\n".format(
os.path.basename(fn[0]), zcegrad_spec['gmax'],
os.path.basename(fn), zcegrad_spec['gmax'],
zcegrad_spec['fwhm'],
np.mean(zcegrad_spec['fwhm_x'])))
for i in range(len(zce_spec['x'])):
......@@ -117,7 +117,7 @@ def print_graph(ds, coff, coffgrad, filename):
widget.close()
def dialog(parent, ds, filename, update_signal):
def dialog(parent, augCanvas, update_signal):
coff = dict(name="", xlabel="Voltage (V)", ylabel="ion count")
coffgrad = dict(c_ymin=-0.1, name="", xlabel="",
ylabel="ion count gradient", gmax=None, fwhm_x=None,
......@@ -129,8 +129,8 @@ def dialog(parent, ds, filename, update_signal):
QtWidgets.QDialog.closeEvent(widget, event)
def update_fnc():
pop_dial(coffspect, coffspect_grad, ds, coff, coffgrad,
textfield, filename, parent)
pop_dial(coffspect, coffspect_grad, augCanvas.ds, coff, coffgrad,
textfield, augCanvas.filename, parent)
dial_widget = QtWidgets.QDialog(
parent, windowTitle='TSQ zero collision energy calculator')
......@@ -151,10 +151,10 @@ def dialog(parent, ds, filename, update_signal):
zce_export = QtWidgets.QPushButton("Export ZCE")
zce_export.clicked.connect(lambda: exp_zce(
coff, coffgrad, filename, parent))
coff, coffgrad, augCanvas.filename, parent))
zce_print = QtWidgets.QPushButton("Print ZCE")
zce_print.clicked.connect(lambda: print_graph(
ds, coff, coffgrad, filename))
augCanvas.ds, coff, coffgrad, augCanvas.filename))
zce_help = QtWidgets.QPushButton("Help")
zce_help.clicked.connect(lambda: help_msg(parent))
close_button = QtWidgets.QPushButton("Close")
......@@ -174,5 +174,5 @@ def dialog(parent, ds, filename, update_signal):
dial_layout.addWidget(graph_canvas)
dial_layout.addLayout(butt_layout)
dial_widget.show()
pop_dial(coffspect, coffspect_grad, ds, coff, coffgrad,
textfield, filename, parent)
pop_dial(coffspect, coffspect_grad, augCanvas.ds, coff, coffgrad,
textfield, augCanvas.filename, parent)
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