drltools.py 31.4 KB
Newer Older
Yan's avatar
Yan committed
1
2
3
4
5
#!/usr/bin/env python3
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from PyQt5 import QtCore
from PyQt5 import QtWidgets
6
from PyQt5 import QtGui
Yan's avatar
Yan committed
7
from PyQt5 import QtPrintSupport
3Yan's avatar
3Yan committed
8
from copy import copy
Yan's avatar
Yan committed
9
10
import matplotlib
import numpy as np
Yan's avatar
Yan committed
11
12
import prasopes.datatools as dt
import prasopes.graphtools as gt
Yan's avatar
Yan committed
13
import prasopes.filetools as ft
3Yan's avatar
3Yan committed
14
import prasopes.config as cf
Yan's avatar
Yan committed
15
import os.path
Yan's avatar
Yan committed
16
import logging
Yan's avatar
Yan committed
17
18
matplotlib.use("Qt5Agg")

Yan's avatar
Yan committed
19

Yan's avatar
Yan committed
20
21
22
logger = logging.getLogger('drlLogger')


Yan's avatar
Yan committed
23
24
class StretchWidget(QtWidgets.QWidget):
    """horizontal stretch class"""
Yan's avatar
Yan committed
25
    def __init__(self):
Yan's avatar
Yan committed
26
        super(StretchWidget, self).__init__()
Yan's avatar
Yan committed
27
        self._main = QtWidgets.QWidget()
Yan's avatar
Yan committed
28
29
        self.setSizePolicy(QtWidgets.QSizePolicy.Expanding
                          ,QtWidgets.QSizePolicy.Preferred)
Yan's avatar
Yan committed
30
31


Yan's avatar
Yan committed
32
def floatize(table, row, column, nonneg=True):
33
34
35
36
    """grabs the tableWidgetItem and transforms its text safely to
    float, if the text is not acceptable as float, returns zero"""
    imptext = table.item(row, column).text()
    validator = QtGui.QDoubleValidator()
Yan's avatar
Yan committed
37
38
    if nonneg == True:
        validator.setBottom(0)
39
40
41
42
43
44
45
46
    status = validator.validate(imptext, 0)[0]
    if status == QtGui.QValidator.Acceptable:
        outfloat = float(imptext)
    else:
        outfloat = 0
    return outfloat


47
48
49
50
51
52
53
def get_massargs(pt, row, ds):
    startm = floatize(pt, row, 1) - (floatize(pt, row, 2) / 2)
    endm = floatize(pt, row, 1) + (floatize(pt, row, 2) / 2)
    massargs = dt.argsubselect(ds['masses'], startm, endm)
    return massargs


54
def update_profile(pt, row, dataset):
Yan's avatar
Yan committed
55
    """parent table profile spectrum updating procedure"""
Yan's avatar
Yan committed
56
    # Dont do anything to graph when the spectrum is not populated
Yan's avatar
Yan committed
57
    logger.debug("updating parent table row {} profile".format(row))
Yan's avatar
Yan committed
58
    if isinstance(dataset['masses'], type(None)):
59
60
        return

61
    spectrum = pt.cellWidget(row, 3).figure.get_axes()[0]
Yan's avatar
Yan committed
62
    masses = dataset['masses']
63
    massargs = get_massargs(pt, row, dataset)
64
    yshape = np.mean(dataset['matrix'], axis=0)
Yan's avatar
Yan committed
65
    spectrum.clear()
66
67
68
    spectrum.plot(masses, yshape, ':', color='gray')
    spectrum.plot(masses[massargs], yshape[massargs], 'r')
    xex = max((masses[massargs[-1]]-masses[massargs[0]])*0.25, 0.20)
Yan's avatar
Yan committed
69
70
71
    spectrum.set_xlim(masses[massargs[0]]-xex,
                      masses[massargs[-1]]+xex)
    ymax = max(yshape[massargs])
72
73
74
    spectrum.set_ylim(ymax*-0.1, ymax*1.2)
    spectrum.figure.canvas.draw()

Yan's avatar
Yan committed
75

3Yan's avatar
3Yan committed
76
def get_intensity(row, ds, drls):
77
    massargs = get_massargs(drls['pt'], row, ds)
Yan's avatar
Yan committed
78
79
80
81
    #prevent division by 0
    intensity = np.divide(np.sum( ds['matrix'].T[massargs].T, axis=1),
            np.clip(ds['chrom_dat'][1], np.nextafter(
                0, 1, dtype=np.float32), None))
Yan's avatar
Yan committed
82
83
84
    return intensity


3Yan's avatar
3Yan committed
85
def get_daughterset(ds, drls):
Yan's avatar
Yan committed
86
87
    """Fuction to acquire the curves of the daugher ions"""
    logger.info("getting set of the daughter ions")
Yan's avatar
Yan committed
88
    names = []
3Yan's avatar
3Yan committed
89
    times = ds['chrom_dat'][0, :] - drls['tshift'].value()
Yan's avatar
Yan committed
90
    intensities = []
3Yan's avatar
3Yan committed
91
92
93
    for row in range(drls['dt'].rowCount()):
        if drls['dt'].cellWidget(row, 0).checkState() == 2:
            intensity = get_intensity(row, ds, drls)
3Yan's avatar
3Yan committed
94
            corlist = []
Yan's avatar
Yan committed
95
            for i in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
96
97
                cor = drls['dt'].cellWidget(row, 1+i*2).currentIndex() - 1
                if cor not in (-2, -1):
Yan's avatar
Yan committed
98
                    factor = floatize(drls['dt'], row, 2+i*2, False)
3Yan's avatar
3Yan committed
99
100
101
102
103
104
                    correction = get_intensity(cor, ds, drls) * factor
                    intensity = intensity - correction
                    corlist.append("{} * {}".format(
                        drls['dt'].item(row,2+i*2).text(),
                        drls['dt'].cellWidget(row,1+i*2).currentText()))
            cortext = " + ".join(corlist)
Yan's avatar
Yan committed
105
            intensities.append(intensity)
3Yan's avatar
3Yan committed
106
            names.append("{} - ({})".format(
3Yan's avatar
3Yan committed
107
                drls['dt'].item(row, 0).text(),
3Yan's avatar
3Yan committed
108
                cortext))
Yan's avatar
Yan committed
109
110
111
    return names, times, intensities


3Yan's avatar
3Yan committed
112
def get_parentset(ds, drls):
113
114
115
116
    names = []
    times = ds['chrom_dat'][0, :]
    intensities = []
    rowlist = []
3Yan's avatar
3Yan committed
117
118
    for row in range(drls['dt'].rowCount()):
        if drls['dt'].cellWidget(row, 0).checkState() == 2:
119
            rowlist.append(row)
3Yan's avatar
3Yan committed
120
121
122
123
124
125
            for corcol in range(drls['cors'].value()):
                if drls['dt'].cellWidget(
                        row, corcol*2 + 1).currentIndex() > 0\
                        and floatize(drls['dt'], row, 2) != 0:
                    rowlist.append(
                        drls['dt'].cellWidget(row, 1).currentIndex()-1)
126
    for row in set(rowlist):
3Yan's avatar
3Yan committed
127
            intensity = get_intensity(row, ds, drls)
128
            intensities.append(intensity)
3Yan's avatar
3Yan committed
129
            names.append(drls['dt'].item(row, 0).text())
130
131
132
    return names, times, intensities


3Yan's avatar
3Yan committed
133
def update_drlspectrum(ds, drls, drlspectrum):
Yan's avatar
Yan committed
134
135
    """Generic DRL spectrum updating procedure"""
    logger.info("updating DRL spectrum")
Yan's avatar
Yan committed
136
    # Do not do anything when the data set is not populated.
Yan's avatar
Yan committed
137
    if isinstance(ds['masses'], type(None)):
Yan's avatar
Yan committed
138
        return
139
    colors = np.array([[0, 0, 0], [255, 0, 0], [0, 255, 0], [0, 0, 255],
140
141
142
                       [0, 200, 255], [255, 200, 0], [255, 100, 0],
                       [200, 50, 0], [255, 0, 200], [0, 100, 0],
                       [0, 100, 255], [100, 100, 100]])
Yan's avatar
Yan committed
143

3Yan's avatar
3Yan committed
144
    names, times, intensities = get_daughterset(ds, drls)
3Yan's avatar
3Yan committed
145
146
147
    drlspectrum.clear()
    gt.pop_plot(drlspectrum, drls['graphlabels'])
    drlspectrum.axvline(0, 0, 0.9, color="#FF000088", linestyle=":")
3Yan's avatar
3Yan committed
148

3Yan's avatar
3Yan committed
149
150
151
152
    if drls['cutoff'].value() != 0:
        drlspectrum.axvline(drls['cutoff'].value(), 0, 0.9,
                            color="#0000FF88", linestyle=":")

153
    i = 0
3Yan's avatar
3Yan committed
154
155
156
157
    for row in range(drls['dt'].rowCount()):
        if drls['dt'].cellWidget(row, 0).checkState() == 2:
            drls['dt'].blockSignals(True)
            drls['dt'].item(row, 0).setBackground(QtGui.QBrush(
158
                QtGui.QColor(*colors[row % len(colors)], alpha=50)))
3Yan's avatar
3Yan committed
159
160
            drls['dt'].blockSignals(False)
            label = " {}".format(drls['pt'].item(row, 0).text())
3Yan's avatar
3Yan committed
161
162
            intensity = intensities[i]
            if drls['rel'].checkState() == 2:
Yan's avatar
Yan committed
163
164
165
                #Do not divide by 0
                intensity = np.divide(intensity, np.clip(np.sum(
                    intensities, 0), np.nextafter(
3Yan's avatar
3Yan committed
166
                        0, 1, dtype=np.float32), None), dtype=np.float64)
3Yan's avatar
3Yan committed
167
            drlspectrum.plot(times, intensity, label=label,
168
169
                             color=(colors[row % len(colors)] / 255))
            i += 1
170
        else:
3Yan's avatar
3Yan committed
171
            drls['dt'].item(row, 0).setBackground(QtGui.QBrush())
172

173
    if len(names) != 0:
3Yan's avatar
3Yan committed
174
175
176
177
        gmax = np.amax(intensities)
        if drls['rel'].checkState() == 2:
            gmax = 1
        drlspectrum.set_ylim(top=gmax*1.1, bottom=gmax*-0.01)
178
        drlspectrum.legend(loc=2)
179
180
    drlspectrum.figure.canvas.draw()

Yan's avatar
Yan committed
181

Yan's avatar
Yan committed
182
def gettableitemlist(ptable):
183
    ion_list = []
Yan's avatar
Yan committed
184
185
186
    for row in range(ptable.rowCount()):
        text = []
        for i in range(3):
187
188
            if not isinstance(ptable.item(row, i), type(None)):
                frg = ptable.item(row, i).text()
Yan's avatar
Yan committed
189
190
191
            else:
                frg = ""
            text.append(frg)
192
        line = "{} ({}; fw={})".format(*text)
Yan's avatar
Yan committed
193
        ion_list.append(line)
194
195
196
    return ion_list


3Yan's avatar
3Yan committed
197
def update_corrfors(drls):
198
    """update corrections selection layout of the daughter table"""
3Yan's avatar
3Yan committed
199
200
    ionlist = gettableitemlist(drls['pt'])
    for row in range(drls['dt'].rowCount()):
Yan's avatar
Yan committed
201
        for i in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
202
203
204
205
206
207
208
209
            corfor = drls['dt'].cellWidget(row, 1+i*2)
            index = corfor.currentIndex()
            corfor.blockSignals(True)
            corfor.clear()
            corfor.addItem("")
            corfor.addItems(ionlist)
            corfor.setCurrentIndex(index)
            corfor.blockSignals(False)
Yan's avatar
Yan committed
210

211

3Yan's avatar
3Yan committed
212
def ptable_changed(row, column, ds, drls, drlspectrum):
213
    """routine called by change of the ptable spectra"""
Yan's avatar
Yan committed
214
    logger.debug("ptable changed routine called")
3Yan's avatar
3Yan committed
215
216
    update_corrfors(drls)
    drls['dt'].item(row, 0).setText(gettableitemlist(drls['pt'])[row])
217
    if column in (1, 2):
3Yan's avatar
3Yan committed
218
        update_profile(drls['pt'], row, ds)
219

220

3Yan's avatar
3Yan committed
221
def dtable_changed(row, column, ds, drls, drlspectrum):
222
    """routine called by change of the dtable spectra"""
Yan's avatar
Yan committed
223
    logger.info("Change in the daughter ion table detected")
3Yan's avatar
3Yan committed
224
    if drls['dt'].cellWidget(row, 0).checkState() == 2:
Yan's avatar
Yan committed
225
226
227
        if (column == 0) or (column % 2 == 0 and drls['dt'].cellWidget(
            row, column-1).currentIndex() != 0):
            update_drlspectrum(ds, drls, drlspectrum)
228

Yan's avatar
Yan committed
229

3Yan's avatar
3Yan committed
230
def corr_changed(correction, ds, drls, drlspectrum):
231
    """routine called by change of correction for ion"""
Yan's avatar
Yan committed
232
    logger.info('''Change of the "correct to" detected''')
3Yan's avatar
3Yan committed
233
234
235
236
    for i in range(drls['dt'].rowCount()):
        for j in range(drls['dt'].columnCount()):
            if correction == drls['dt'].cellWidget(i, 1+j*2):
                row, column = i, 1 + j*2
Yan's avatar
Yan committed
237
238
239
                logger.debug('''Change of the "correct to" on '''
                             '''row {}, column {}'''.format(
                                 row + 1, column + 1))
3Yan's avatar
3Yan committed
240
    if (drls['dt'].cellWidget(row, 0).checkState() == 2
3Yan's avatar
3Yan committed
241
       and floatize(drls['dt'], row, column+1, False) != 0):
3Yan's avatar
3Yan committed
242
        update_drlspectrum(ds, drls, drlspectrum)
243
244


Yan's avatar
Yan committed
245
246
247
def corcount_changed(ds, drls, drlspectrum):
    """routine called by change of the correction factors count"""
    logger.info('''change in the correction count detected''')
3Yan's avatar
3Yan committed
248
249
    diff = int(drls['cors'].value() -
                  ((drls['dt'].columnCount() - 1) / 2))
Yan's avatar
Yan committed
250
251
252
    if diff == 0:
        return
    elif diff > 0:
3Yan's avatar
3Yan committed
253
        drls['dt'].blockSignals(True)
Yan's avatar
Yan committed
254
255
256
257
258
259
260
261
        drls['dt'].setColumnCount(1 + (drls['cors'].value() * 2))
        newcors = []
        for col in range(drls['dt'].columnCount() - (diff * 2),
                       drls['dt'].columnCount(), 2):
            for row in range(drls['dt'].rowCount()):
                    drls['dt'].setCellWidget(
                        row, col, QtWidgets.QComboBox())
                    drls['dt'].cellWidget(row, col).setFrame(False)
3Yan's avatar
3Yan committed
262
263
                    drls['dt'].cellWidget(row, col).setFocusPolicy(
                            QtCore.Qt.NoFocus)
Yan's avatar
Yan committed
264
265
266
267
268
269
270
271
272
273
274
                    drls['dt'].setItem(
                        row, col+1, QtWidgets.QTableWidgetItem())
                    newcors.append(drls['dt'].cellWidget(row, col))
        list(map(lambda x: x.currentIndexChanged.connect(lambda:
            corr_changed(x, ds, drls, drlspectrum)), newcors))
        update_corrfors(drls)
        dcolums = ["Name"]
        for i in range(drls['cors'].value()):
            dcolums.append("corrected for ({})".format(i+1))
            dcolums.append("factor ({})".format(i+1))
        drls['dt'].setHorizontalHeaderLabels(dcolums)
3Yan's avatar
3Yan committed
275
        drls['dt'].blockSignals(False)
Yan's avatar
Yan committed
276
    else:
3Yan's avatar
3Yan committed
277
        drls['dt'].blockSignals(True)
Yan's avatar
Yan committed
278
        drls['dt'].setColumnCount(1 + (drls['cors'].value() * 2))
3Yan's avatar
3Yan committed
279
        drls['dt'].blockSignals(False)
Yan's avatar
Yan committed
280
281
282
        update_drlspectrum(ds, drls, drlspectrum)


3Yan's avatar
3Yan committed
283
def remove_rows(ds, drls, drlspectrum, rows=None):
3Yan's avatar
3Yan committed
284
    logger.info("remowing rows")
285
286
    if rows == None:
        rows = reversed(list(set(
3Yan's avatar
3Yan committed
287
            map(lambda x: x.row(), drls['pt'].selectedIndexes()))))
288
    cors = []
289
    for row in rows:
3Yan's avatar
3Yan committed
290
291
292
293
        drls['dt'].cellWidget(row,0).setCheckState(0)
        drls['dt'].removeRow(row)
        drls['pt'].removeRow(row)
        for i in range(drls['dt'].rowCount()):
Yan's avatar
Yan committed
294
            for cornum in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
295
                corfor = drls['dt'].cellWidget(i, 1+cornum*2)
3Yan's avatar
3Yan committed
296
                cors.append(corfor)
3Yan's avatar
3Yan committed
297
298
299
300
301
302
303
                corfor.disconnect()
                index = corfor.currentIndex()
                corfor.clear()
                corfor.addItem("")
                corfor.addItems(gettableitemlist(drls['pt']))
                if index == row+1:
                    corfor.setCurrentIndex(0)
3Yan's avatar
3Yan committed
304
                    corr_changed(corfor, ds, drls, drlspectrum)
3Yan's avatar
3Yan committed
305
306
307
308
                elif index > row+1:
                    corfor.setCurrentIndex(index-1)
                else:
                    corfor.setCurrentIndex(index)
Yan's avatar
Yan committed
309
310
        list(map(lambda x: x.currentIndexChanged.connect(lambda:
            corr_changed(x, ds, drls, drlspectrum)), cors))
311
312


3Yan's avatar
3Yan committed
313
def add_line(ds, drls, drlspectrum):
314
    """add parent ion to the table"""
Yan's avatar
Yan committed
315
    logger.debug("adding line")
3Yan's avatar
3Yan committed
316
    newrow = drls['pt'].rowCount()
317

3Yan's avatar
3Yan committed
318
319
    drls['pt'].blockSignals(True)
    drls['dt'].blockSignals(True)
320

3Yan's avatar
3Yan committed
321
    drls['pt'].setRowCount(newrow + 1)
322
    for i in range(3):
3Yan's avatar
3Yan committed
323
        drls['pt'].setItem(newrow, i, QtWidgets.QTableWidgetItem())
324
        if newrow is not 0:
3Yan's avatar
3Yan committed
325
326
327
328
            val = floatize(drls['pt'], newrow-1, i)
            if i != 2:
                val = val+1
            drls['pt'].item(newrow, i).setText(str(val))
329

330
    ion_graph = Figure(figsize=(3, 1.5), dpi=100, facecolor="None")
331
332
    ion_graph.add_subplot(111, facecolor=(1, 1, 1, 0.8),
                          position=(-0.01, -0.01, 1.02, 1.02))
333
334
335
    graph_canvas = FigureCanvas(ion_graph)
    graph_canvas.setStyleSheet("background-color:transparent;")
    graph_canvas.setAutoFillBackground(False)
3Yan's avatar
3Yan committed
336
    drls['pt'].setCellWidget(newrow, 3, graph_canvas)
337

3Yan's avatar
3Yan committed
338
    drls['dt'].setRowCount(newrow + 1)
Yan's avatar
Yan committed
339
    checkbox = QtWidgets.QCheckBox()
3Yan's avatar
3Yan committed
340
    checkbox.setFocusProxy(drls['dt'])
341
342
    dname = QtWidgets.QTableWidgetItem()
    dname.setFlags(dname.flags() & ~QtCore.Qt.ItemIsEditable)
Yan's avatar
Yan committed
343
    dname.setTextAlignment(QtCore.Qt.AlignRight)
3Yan's avatar
3Yan committed
344
345
    drls['dt'].setItem(newrow, 0, dname)
    drls['dt'].setCellWidget(newrow, 0, checkbox)
3Yan's avatar
3Yan committed
346

Yan's avatar
Yan committed
347
    for i in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
348
349
        col = copy(1+i*2)
        drls['dt'].setCellWidget(newrow, col, QtWidgets.QComboBox())
3Yan's avatar
3Yan committed
350
        drls['dt'].cellWidget(newrow, col).setFocusPolicy(QtCore.Qt.NoFocus)
3Yan's avatar
3Yan committed
351
352
        drls['dt'].cellWidget(newrow, col).setFrame(False)
        drls['dt'].setItem(newrow, col+1, QtWidgets.QTableWidgetItem())
353

3Yan's avatar
3Yan committed
354
355
    drls['pt'].blockSignals(False)
    drls['dt'].blockSignals(False)
356

3Yan's avatar
3Yan committed
357
    cors = list(map(lambda x: drls['dt'].cellWidget(newrow, 1+x*2),
Yan's avatar
Yan committed
358
                    range(drls['cors'].value())))
3Yan's avatar
3Yan committed
359
360
361
    list(map(lambda x: x.currentIndexChanged.connect(lambda:
        corr_changed(x, ds, drls, drlspectrum)), cors))

3Yan's avatar
3Yan committed
362
    ptable_changed(newrow, 1, ds, drls, drlspectrum)
363
    select_all_btn_up(ds, drls, drlspectrum)
364

Yan's avatar
Yan committed
365
    checkbox.stateChanged.connect(lambda: update_drlspectrum(
3Yan's avatar
3Yan committed
366
        ds, drls, drlspectrum))
367
368
    checkbox.stateChanged.connect(lambda: select_all_btn_up(
        ds, drls, drlspectrum))
369
370


Yan's avatar
Yan committed
371
def iontable(labels):
372
373
    """creates a table for ions"""
    table = QtWidgets.QTableWidget(columnCount=len(labels))
374
    table.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
375
376
                        QtWidgets.QSizePolicy.Expanding)
    table.setHorizontalHeaderLabels(labels)
377
378
379
380
381
    table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)

    for n in range(table.columnCount()):
        table.horizontalHeader().setSectionResizeMode(
            n, QtWidgets.QHeaderView.Stretch)
Yan's avatar
Yan committed
382
    table.setMinimumSize(600, 0)
383

384
    return table
385
386


3Yan's avatar
3Yan committed
387
def load_drltables(parent, dataset, drls, drlspectrum):
Yan's avatar
Yan committed
388
389
    filename = QtWidgets.QFileDialog.getOpenFileName(
            caption="Load DRL config tables",
3Yan's avatar
3Yan committed
390
391
            filter="comma-separated values (*.csv)",
            directory=cf.settings().value("open_folder"))[0]
Yan's avatar
Yan committed
392
393
    if filename is not '':
        names = []
394
395
        masses = []
        peak_widths = []
Yan's avatar
Yan committed
396
        states = []
3Yan's avatar
3Yan committed
397
        corrections = []
Yan's avatar
Yan committed
398

3Yan's avatar
3Yan committed
399

Yan's avatar
Yan committed
400
401
        with open(filename, 'r') as cfile:
            rawdata = cfile.read().splitlines()
3Yan's avatar
3Yan committed
402
403
        for i in range(len(rawdata[0].split(","))-4):
            corrections.append([])
Yan's avatar
Yan committed
404
405
        for i in range(1, len(rawdata)):
            rawline = rawdata[i].split(",")
Yan's avatar
Yan committed
406
            n = len(rawline)
3Yan's avatar
3Yan committed
407
            if n < 4 or not n % 2 == 0 or (rawline[3] not in map(
3Yan's avatar
3Yan committed
408
                str,range(3))) or not (set(map(int, rawline[4:n:2]))
3Yan's avatar
3Yan committed
409
                & set(range(-1, n)) or (n == 4)):
Yan's avatar
Yan committed
410
411
                QtWidgets.QMessageBox.warning(
                    parent, "Load DRL config tables",
3Yan's avatar
3Yan committed
412
413
414
                    "Wrong or corrupted config file.\n"
                    "Error encountered on line {}.\n"
                    "Cancelling request.".format(i+1))
Yan's avatar
Yan committed
415
                return
416
            for j, k in enumerate((names, masses, peak_widths,
3Yan's avatar
3Yan committed
417
                                   states, *corrections)):
3Yan's avatar
3Yan committed
418
419
                if len(rawline) > j:
                    k.append(rawline[j])
3Yan's avatar
3Yan committed
420
421
422
        for row in reversed(range(drls['pt'].rowCount())):
            drls['dt'].removeRow(row)
            drls['pt'].removeRow(row)
423
        # first populate only the parent table
Yan's avatar
Yan committed
424
        for i in range(len(names)):
3Yan's avatar
3Yan committed
425
426
            add_line(dataset, drls, drlspectrum)
            drls['pt'].item(i, 0).setText(names[i])
427
428
            drls['pt'].item(i, 1).setText(masses[i])
            drls['pt'].item(i, 2).setText(peak_widths[i])
429
        # and after that the daughter table
3Yan's avatar
3Yan committed
430
        drls['cors'].setValue(int((len(corrections) / 2)))
Yan's avatar
Yan committed
431
        for i in range(len(names)):
3Yan's avatar
3Yan committed
432
            for j in range(int((len(rawline)-4)/2)):
3Yan's avatar
3Yan committed
433
                drls['dt'].cellWidget(i, 1+j*2).setCurrentIndex(
3Yan's avatar
3Yan committed
434
435
                    int(corrections[0+j*2][i]))
                drls['dt'].item(i, 2+j*2).setText(corrections[1+j*2][i])
3Yan's avatar
3Yan committed
436
            drls['dt'].cellWidget(i, 0).setCheckState(int(states[i]))
Yan's avatar
Yan committed
437
438


3Yan's avatar
3Yan committed
439
def save_drlconfig(drls, parent, exp_f_name=None):
Yan's avatar
Yan committed
440
    """safe DRL table layout so it can be summoned when needed"""
441
442
443
444
    if exp_f_name == None:
        exp_f_name = ft.get_save_filename(
            "Save DRL table layout", "comma-separated values (*.csv)",
            "csv", parent)
Yan's avatar
Yan committed
445
    if exp_f_name is not '':
3Yan's avatar
3Yan committed
446
        corlist = []
Yan's avatar
Yan committed
447
        for i in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
448
449
450
            corlist.append("corrected_to_{}, factor_{} ".format(
                i+1, i+1))
        cortext = ", ".join(corlist)
Yan's avatar
Yan committed
451
        expf = open(exp_f_name, 'w')
452
        expf.write("#ion_name, m/z, peak_width, visible,"
3Yan's avatar
3Yan committed
453
                   "{}\n".format(cortext))
3Yan's avatar
3Yan committed
454
        for row in range(drls['pt'].rowCount()):
Yan's avatar
Yan committed
455
456
            vals = []
            for i in range(3):
3Yan's avatar
3Yan committed
457
458
                vals.append(drls['pt'].item(row, i).text())
            vals.append(drls['dt'].cellWidget(row, 0).checkState())
Yan's avatar
Yan committed
459
            for i in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
460
461
                vals.append(drls['dt'].cellWidget(row, 1+i*2).currentIndex())
                vals.append(drls['dt'].item(row, 2+i*2).text())
Yan's avatar
Yan committed
462
463
464
            expf.write("{}\n".format((",".join(map(str, vals)))))
        expf.close()

Yan's avatar
Yan committed
465

3Yan's avatar
3Yan committed
466
def export_drlspectrum(parent, fn, ds, drls):
Yan's avatar
Yan committed
467
468
    if fn[0] is None:
        QtWidgets.QMessageBox.warning(
Yan's avatar
Yan committed
469
470
            None, "Export DRL dat aset",
            "No file opened. Nothing to export, canceling request")
Yan's avatar
Yan committed
471
        return
3Yan's avatar
3Yan committed
472
    names, times, intensities = get_daughterset(ds, drls)
3Yan's avatar
3Yan committed
473
474
475
476
    if drls['cutoff'].value() == 0:
        subset = np.where(times > 0)[0]
    else:
        subset = np.where((times > 0) & (times < drls['cutoff'].value()))[0]
3Yan's avatar
3Yan committed
477
    times = times[subset]
Yan's avatar
Yan committed
478
    intensities = list(map(lambda x: x[subset], intensities))
3Yan's avatar
3Yan committed
479
480

    pnames, ptimes, pintensities = get_parentset(ds, drls)
481
482
    if names == []:
        QtWidgets.QMessageBox.warning(
Yan's avatar
Yan committed
483
484
485
            None, "Export DRL data set",
            "No rows in the Corrected ions table selected. "
            "Nothing to export, canceling request")
486
487
488
489
        return
    fname = QtWidgets.QFileDialog.getSaveFileName(
            None,"Export DRL data",
        options=(QtWidgets.QFileDialog.DontConfirmOverwrite |
Yan's avatar
Yan committed
490
        QtWidgets.QFileDialog.HideNameFilterDetails),
3Yan's avatar
3Yan committed
491
        directory=fn[0][:-4])[0]
492
493
494
495
496
    if fname is '':
        return
    exp_f_name = list(map(lambda x: "{}/{}-{}.csv".format(
        fname, os.path.basename(fname), x),
        ["raw", "corrected", "input"]))
Yan's avatar
Yan committed
497
498
499
500
501
502
503
504
505
506
    for name in exp_f_name:
        if os.path.isfile(name):
            quest = QtWidgets.QMessageBox.warning(
                parent, "Export DRL data",
                "File {} already exists in the filesystem.\n"
                "Do you want to overwrite it?"
                .format(os.path.basename(name)),
                QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
            if quest == QtWidgets.QMessageBox.No:
                return
507
508
509
510
511
    if not os.path.exists(fname):
        os.makedirs(fname)
    for i, table in enumerate([[pnames, pintensities],
                               [names, intensities]]):
        expf = open(exp_f_name[i], 'w')
Yan's avatar
Yan committed
512
        expf.write("times,{}\n".format((",".join(table[0]))))
3Yan's avatar
3Yan committed
513
514
        expf.write("timeshift = {}, cutoff = {}\n".format(
            drls['tshift'].value(), drls['cutoff'].value()))
515
        for j in range(len(times)):
Yan's avatar
Yan committed
516
            dataset = list()
517
518
519
            dataset.append(times[j])
            for intensity in table[1]:
                dataset.append(intensity[j])
Yan's avatar
Yan committed
520
521
            expf.write("{}\n".format((",".join(map(str, dataset)))))
        expf.close()
3Yan's avatar
3Yan committed
522
    save_drlconfig(drls, parent, exp_f_name[2])
Yan's avatar
Yan committed
523

Yan's avatar
Yan committed
524

3Yan's avatar
3Yan committed
525
def print_graph(labels, ds, drls):
Yan's avatar
Yan committed
526
    printfig = Figure(figsize=(5, 2), dpi=100)
Yan's avatar
Yan committed
527
528
529
    printplot = printfig.add_subplot(111)
    printcanvas = FigureCanvas(printfig)
    gt.pop_plot(printplot, labels)
3Yan's avatar
3Yan committed
530
    update_drlspectrum(ds, drls, printplot)
Yan's avatar
Yan committed
531
    widget = QtWidgets.QDialog(None, windowTitle='Print preview')
Yan's avatar
Yan committed
532
533
    layout = QtWidgets.QVBoxLayout(widget)
    layout.addWidget(printcanvas)
Yan's avatar
Yan committed
534
    widget.resize(600, 400)
Yan's avatar
Yan committed
535
536
537
538
539
540
541
    widget.show()
    dialog = QtPrintSupport.QPrintDialog()
    if dialog.exec_() == QtWidgets.QDialog.Accepted:
        printcanvas.render(dialog.printer())
    widget.close()


3Yan's avatar
3Yan committed
542
def clip_range(drls):
3Yan's avatar
3Yan committed
543
544
    """copy selected part of the table"""
    logger.debug("copying selected table cells to clipboard")
545
    activeObject = QtWidgets.QApplication.focusWidget()
3Yan's avatar
3Yan committed
546
    if activeObject in (drls['pt'], drls['dt']):
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
        table = activeObject
        if len(table.selectedRanges()) == 0:
            return
        if len(table.selectedRanges()) > 1:
            QtWidgets.QMessageBox.warning(
                None, "Operation not supported",
                "Operation not supported for multiple ranges,\n"
                "cancelling request")
            return
        sr = table.selectedRanges()[0]
        rows = []
        for row in range(sr.topRow(), sr.bottomRow() + 1):
            line = []
            for col in range(sr.leftColumn(), sr.rightColumn() + 1):
                if isinstance(table.cellWidget(row, col),
                            QtWidgets.QComboBox):
                    line.append(
                        table.cellWidget(row, col).currentText())
                elif isinstance(table.item(row, col),
                              QtWidgets.QTableWidgetItem):
                    line.append(table.item(row, col).text())
            rows.append(("\t").join(line))
        QtWidgets.QApplication.clipboard().setText(("\n").join(rows))


3Yan's avatar
3Yan committed
572
def paste_clip(ds, drls, drlspectrum):
3Yan's avatar
3Yan committed
573
    logger.debug("pasting data from clipboard")
574
    activeObject = QtWidgets.QApplication.focusWidget()
3Yan's avatar
3Yan committed
575
    if activeObject in (drls['pt'], drls['dt'])\
576
577
578
579
580
581
582
        and activeObject.selectedRanges() != []:
        table = activeObject
        if len(table.selectedRanges()) > 1:
            QtWidgets.QMessageBox.warning(
                None, "Operation not supported",
                "Operation not supported for multiple ranges,\n"
                "cancelling request")
3Yan's avatar
3Yan committed
583
            return
584
585
586
587
588
589
590
        cliptext = QtWidgets.QApplication.clipboard().text()
        rows = cliptext.split("\n")
        startrow = table.selectedRanges()[0].topRow()
        startcol = table.selectedRanges()[0].leftColumn()
        for i, row in enumerate(rows, start=startrow):
            cols = row.split("\t")
            for j, col in enumerate(cols, start=startcol):
3Yan's avatar
3Yan committed
591
                if table == drls['pt'] and j < 3:
592
                    if i >= (table.rowCount()):
3Yan's avatar
3Yan committed
593
                        add_line(ds, drls, drlspectrum)
594
                    table.item(i, j).setText(col)
595
                if table == drls['dt'] and j != 0 and j % 2 == 0\
596
597
598
599
                     and i < table.rowCount():
                     table.item(i,j).setText(col)


3Yan's avatar
3Yan committed
600
def key_pressed(event, ds, drls, drlspectrum):
601
    if event.key() == QtCore.Qt.Key_Delete:
602
        rows = reversed(list(map(lambda x: x.row(),
3Yan's avatar
3Yan committed
603
604
            drls['pt'].selectionModel().selectedRows())))
        remove_rows(ds, drls, drlspectrum, rows)
Yan's avatar
Yan committed
605
    if event.key() == QtCore.Qt.Key_F5:
3Yan's avatar
3Yan committed
606
607
608
        update_drlspectrum(ds, drls, drlspectrum)
        for row in range(drls['pt'].rowCount()):
            update_profile(drls['pt'], row, ds)
609
610
    if event.key() == QtCore.Qt.Key_C\
        and event.modifiers().__int__() == QtCore.Qt.ControlModifier:
3Yan's avatar
3Yan committed
611
        clip_range(drls)
612
613
    if event.key() == QtCore.Qt.Key_V\
        and event.modifiers().__int__() == QtCore.Qt.ControlModifier:
3Yan's avatar
3Yan committed
614
        paste_clip(ds, drls, drlspectrum)
615

Yan's avatar
Yan committed
616

617
618
def select_all_btn_up(ds, drls, drlspectrum, state=None):
    logger.info('''Change of the select-all button detected''')
619
620
621
622
623
624
625
626
627
628
    if state in (0,2):
        for row in range(drls['dt'].rowCount()):
            drls['dt'].cellWidget(row, 0).blockSignals(True)
            drls['dt'].cellWidget(row, 0).setCheckState(state)
            drls['dt'].cellWidget(row, 0).blockSignals(False)
        update_drlspectrum(ds, drls, drlspectrum)
    elif state == 1:
        drls['checkAll'].setCheckState(2)
    else:
        drls['checkAll'].blockSignals(True)
629
630
631
        btns = []
        for row in range(drls['dt'].rowCount()):
            btns.append(drls['dt'].cellWidget(row, 0).checkState())
632
        if all(btns):
633
            drls['checkAll'].setCheckState(2)
634
635
        elif any(btns):
            drls['checkAll'].setCheckState(1)
636
637
        else:
            drls['checkAll'].setCheckState(0)
638
        drls['checkAll'].blockSignals(False)
639

640

641
def main_window(parent, ds, filename, cache, update_signal):
642
    """constructs a dialog window"""
643
    def onclose(widget, event, buffer, drls, canvas, update_fnc):
3Yan's avatar
3Yan committed
644
        buffer[0], buffer[1] = drls, canvas
645
        update_signal.signal.disconnect(update_fnc)
Yan's avatar
Yan committed
646
        QtWidgets.QMainWindow.closeEvent(widget, event)
Yan's avatar
Yan committed
647

648
649
650
    def update_fnc():
        update_drlspectrum(ds, drls, chromplot)

Yan's avatar
Yan committed
651
    window = QtWidgets.QMainWindow(
Yan's avatar
Yan committed
652
        parent, windowTitle='Delayed reactant labeling')
Yan's avatar
Yan committed
653
654
    main_widget = QtWidgets.QWidget(window)
    window.setCentralWidget(main_widget)
Yan's avatar
Yan committed
655

656
657
    window.closeEvent = lambda event: onclose(
        window, event, cache, drls, graph_canvas, update_fnc)
Yan's avatar
Yan committed
658

3Yan's avatar
3Yan committed
659
660
661
    time_title = QtWidgets.QLabel("Time shift (min):")
    drls['tshift'] = QtWidgets.QDoubleSpinBox(
            minimum=-100, maximum=1440, decimals=3)
3Yan's avatar
3Yan committed
662
663
664
    cutoff_title = QtWidgets.QLabel("Cut off (min):")
    drls['cutoff'] = QtWidgets.QDoubleSpinBox(
            minimum=0, maximum=1440, decimals=3)
3Yan's avatar
3Yan committed
665
    drls['rel'] = QtWidgets.QCheckBox("Steady state approximation")
666
    drls['checkAll'] = QtWidgets.QCheckBox("Select all")
Yan's avatar
Yan committed
667
    drls['cors'] = QtWidgets.QSpinBox(minimum=0)
668

669
670
671
    drl_load = QtWidgets.QPushButton("&Load")
    drl_save = QtWidgets.QPushButton("&Save")
    drl_export = QtWidgets.QPushButton("&Export")
Yan's avatar
Yan committed
672
    drl_print = QtWidgets.QPushButton("&Print")
673
    close = QtWidgets.QPushButton("&Close")
Yan's avatar
Yan committed
674
    close.clicked.connect(window.close)
675

Yan's avatar
Yan committed
676
677
678
    btn_add = QtWidgets.QPushButton("&Add")
    btn_rem = QtWidgets.QPushButton("Remove")

3Yan's avatar
3Yan committed
679
    if cache == [None, None]:
3Yan's avatar
3Yan committed
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
        dial_graph = Figure(figsize=(5, 2), dpi=100, facecolor="None")
        chromplot = dial_graph.add_subplot(111, facecolor=(1, 1, 1, 0.8))
        graph_canvas = FigureCanvas(dial_graph)
        graph_canvas.setStyleSheet("background-color:transparent;")
        graph_canvas.setAutoFillBackground(False)
        drls['graphlabels'] = dict(x=[0], y=[0], line=None, name="",
                                   xlabel="time(min)",
                                   ylabel="relative intensity")
        gt.pan_factory(chromplot)
        gt.zoom_factory(chromplot, 1.15)
        gt.pop_plot(chromplot, drls['graphlabels'])

        # pt = parenttable
        # dt = daughtertable
        drls = dict(pt=None, dt=None, tshift=None, cutoff=None, cors=None,
                rel=None, checkAll=None)


3Yan's avatar
3Yan committed
698
        dcolums = ["Name"]
Yan's avatar
Yan committed
699
700
        drls['cors'].setValue(3)
        for i in range(drls['cors'].value()):
3Yan's avatar
3Yan committed
701
702
703
            dcolums.append("corrected for ({})".format(i+1))
            dcolums.append("factor ({})".format(i+1))
        drls['dt'] = iontable(dcolums)
704
        drls['pt'] = iontable(["Name", "Mass (m/z)", "Peak width",
3Yan's avatar
3Yan committed
705
                               "profile"])
3Yan's avatar
3Yan committed
706
707
708
709
        #TODO: DIRTY, DIRTY, DIRTY !!! do it nicer when I'll know how i want it
        for n in range(drls['dt'].columnCount()):
            drls['dt'].horizontalHeader().setSectionResizeMode(
                n, QtWidgets.QHeaderView.Interactive)
3Yan's avatar
3Yan committed
710
        add_line(ds, drls, chromplot)
Yan's avatar
Yan committed
711
    else:
3Yan's avatar
3Yan committed
712
713
        drls = cache[0]
        graph_canvas = cache[1]
3Yan's avatar
3Yan committed
714
        chromplot = graph_canvas.figure.axes[0]
715

716
    window.keyPressEvent = lambda event: key_pressed(
3Yan's avatar
3Yan committed
717
        event, ds, drls, chromplot)
718

719
    btn_add.clicked.connect(lambda: add_line(
3Yan's avatar
3Yan committed
720
        ds, drls, chromplot))
721
    btn_rem.clicked.connect(lambda: remove_rows(
3Yan's avatar
3Yan committed
722
        ds, drls, chromplot))
Yan's avatar
Yan committed
723
    drl_load.clicked.connect(lambda: load_drltables(
3Yan's avatar
3Yan committed
724
        main_widget, ds, drls, chromplot))
Yan's avatar
Yan committed
725
    drl_save.clicked.connect(lambda: save_drlconfig(
3Yan's avatar
3Yan committed
726
        drls, main_widget))
Yan's avatar
Yan committed
727
    drl_print.clicked.connect(lambda: print_graph(
3Yan's avatar
3Yan committed
728
        graphlabels, ds, drls))
Yan's avatar
Yan committed
729
    drl_export.clicked.connect(lambda: export_drlspectrum(
3Yan's avatar
3Yan committed
730
731
732
733
734
735
        main_widget, filename, ds, drls))

    drls['pt'].itemChanged.connect(lambda item: ptable_changed(
        item.row(), item.column(), ds, drls, chromplot))
    drls['dt'].itemChanged.connect(lambda item: dtable_changed(
        item.row(), item.column(), ds, drls, chromplot))
736
737
    drls['tshift'].valueChanged.connect(update_fnc)
    drls['cutoff'].valueChanged.connect(update_fnc)
Yan's avatar
Yan committed
738
739
    drls['cors'].valueChanged.connect(lambda: corcount_changed(
        ds, drls, chromplot))
740
    drls['rel'].stateChanged.connect(update_fnc)
741
742
    drls['checkAll'].stateChanged.connect(lambda state:
        select_all_btn_up(ds, drls, chromplot, state))
743
    update_signal.signal.connect(update_fnc)
744

745
746
747
748
749
750
751
752
753
    actionBar = QtWidgets.QToolBar(window)
    window.addToolBar(QtCore.Qt.BottomToolBarArea, actionBar)
    actionBar.setAllowedAreas(QtCore.Qt.BottomToolBarArea)
    actionBar.setFloatable(False)
    actionBar.setMovable(False)
    actionBar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
    actionBar.addWidget(drl_load)
    actionBar.addWidget(drl_save)
    actionBar.addWidget(drl_print)
Yan's avatar
Yan committed
754
    actionBar.addWidget(StretchWidget())
755
756
757
758
759
760
761
    actionBar.addWidget(drl_export)
    actionBar.addWidget(close)

    dtdock = QtWidgets.QDockWidget()
    dtdock.setWidget(QtWidgets.QWidget())
    dtdock_layout = QtWidgets.QVBoxLayout(dtdock.widget())
    dtdock.setWindowTitle("Corrected ions table")
Yan's avatar
Yan committed
762
763
764
765
766
767
768
    dt_butlayout = QtWidgets.QHBoxLayout()
    dt_butlayout.addWidget(drls['checkAll'])
    dt_butlayout.addWidget(StretchWidget())
    dt_butlayout.addWidget(QtWidgets.QLabel("Number of corrections:"))
    dt_butlayout.addWidget(drls['cors'])
    dt_butlayout.addWidget(StretchWidget())
    dtdock_layout.addLayout(dt_butlayout)
769
    dtdock_layout.addWidget(drls['dt'])
Yan's avatar
Yan committed
770
    window.addDockWidget(QtCore.Qt.BottomDockWidgetArea, dtdock)
771
772
773
774
775
776

    ptdock = QtWidgets.QDockWidget()
    ptdock.setWidget(QtWidgets.QWidget())
    ptdock_layout = QtWidgets.QVBoxLayout(ptdock.widget())
    ptdock.setWindowTitle("Raw ions table")
    ptdock_layout.addWidget(drls['pt'])
Yan's avatar
Yan committed
777
778
779
780
    pt_butlayout = QtWidgets.QHBoxLayout()
    pt_butlayout.addWidget(btn_add)
    pt_butlayout.addWidget(btn_rem)
    pt_butlayout.addStretch(0)
781
782
783
784
785
786
787
    ptdock_layout.addLayout(pt_butlayout)
    window.addDockWidget(QtCore.Qt.RightDockWidgetArea, ptdock)

    main_layout = QtWidgets.QVBoxLayout(main_widget)
    graphparams_layout = QtWidgets.QHBoxLayout()
    main_layout.addWidget(graph_canvas, stretch=1)
    main_layout.addLayout(graphparams_layout)
3Yan's avatar
3Yan committed
788
789
790
    graphparams_layout.addWidget(time_title)
    graphparams_layout.addWidget(drls['tshift'])
    graphparams_layout.addStretch(1)
3Yan's avatar
3Yan committed
791
792
793
    graphparams_layout.addWidget(cutoff_title)
    graphparams_layout.addWidget(drls['cutoff'])
    graphparams_layout.addStretch(1)
3Yan's avatar
3Yan committed
794
795
    graphparams_layout.addWidget(drls['rel'])
    graphparams_layout.addStretch(1)
796
797


Yan's avatar
Yan committed
798
    window.show()