drltools.py 16.4 KB
Newer Older
Yan's avatar
Yan committed
1
2
3
4
5
6
7
#!/usr/bin/env python3

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.widgets import SpanSelector
from PyQt5 import QtCore
from PyQt5 import QtWidgets
8
from PyQt5 import QtGui
Yan's avatar
Yan committed
9
10
11
import sys
import matplotlib
import numpy as np
Yan's avatar
Yan committed
12
13
import prasopes.datatools as dt
import prasopes.graphtools as gt
Yan's avatar
Yan committed
14
import prasopes.filetools as ft
Yan's avatar
Yan committed
15
16
17
matplotlib.use("Qt5Agg")

class HBar(QtWidgets.QFrame):
18
    """horizontal bar class"""
Yan's avatar
Yan committed
19
20
21
22
23
24
    def __init__(self):
        super(HBar, self).__init__()
        self._main = QtWidgets.QWidget()
        self.setFrameShape(QtWidgets.QFrame.HLine)


Yan's avatar
Yan committed
25
def update_profile(start, end, spectrum, dataset):
26
27
    """spectrum updating procedure"""
    #Dont do anything to graph when the spectrum is not populated
Yan's avatar
Yan committed
28
    if (type(dataset['masses'])) == type(None):
29
30
        return

Yan's avatar
Yan committed
31
32
    masses = dataset['masses']
    massargs = dt.argsubselect(masses, start, end)
33
    yshape = np.mean(dataset['matrix'], axis=0)
Yan's avatar
Yan committed
34
35
    spectrum.clear()
    dots_x = masses
36
    dots_y = yshape
Yan's avatar
Yan committed
37
38
    full_x = masses[massargs]
    full_y = yshape[massargs]
39
40
    spectrum.plot(dots_x, dots_y, ':', color='gray')
    spectrum.plot(full_x, full_y, 'r')
Yan's avatar
Yan committed
41
42
43
44
    xex = (masses[massargs[-1]]-masses[massargs[0]])*0.25
    spectrum.set_xlim(masses[massargs[0]]-xex,
                      masses[massargs[-1]]+xex)
    ymax = max(yshape[massargs])
45
46
47
    spectrum.set_ylim(ymax*-0.1, ymax*1.2)
    spectrum.figure.canvas.draw()

Yan's avatar
Yan committed
48

Yan's avatar
Yan committed
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
def get_daughterset(ptable, dtable, ds):
    names = []
    times = ds['chrom_dat'][0,:]
    intensities = []
    #TODO: resolve intensities trouble
    for row in range(dtable.rowCount()):
        if dtable.cellWidget(row, 1).checkState() == 2:
            startm = dt.floatize(ptable.cellWidget(row,1).text())
            endm = dt.floatize(ptable.cellWidget(row,2).text())
            massargs = dt.argsubselect(ds['masses'], startm, endm)
            intensity = (np.sum(
                ds['matrix'].T[massargs].T, axis=1)) / ds['chrom_dat'][1]
            cor = dtable.cellWidget(row, 2).currentIndex()-1
            if cor != -1:
                factor = dt.floatize(dtable.cellWidget(row,3).text())
                startm = dt.floatize(ptable.cellWidget(cor,1).text())
                endm = dt.floatize(ptable.cellWidget(cor,2).text())
                massargs = dt.argsubselect(ds['masses'], startm, endm)
Yan's avatar
Yan committed
67
                correction = ((np.sum(
Yan's avatar
Yan committed
68
                    ds['matrix'].T[massargs].T, axis=1))\
Yan's avatar
Yan committed
69
70
                              / ds['chrom_dat'][1]) * factor
                intensity = intensity - correction
Yan's avatar
Yan committed
71
72
73
74
75
76
77
78
79
            intensities.append(intensity)
            names.append(dtable.item(row,1).text())
    return names, times, intensities


def update_drlspectrum(ptable, dtable, ds, drlspectrum):
    #Dont do when the dataset is not populated
    if (type(ds['masses'])) == type(None):
        return
80
    colors = np.array([[255,0,0],[0,255,0],[0,0,255],[0,200,255],[255,0,255],[255,200,0]])
Yan's avatar
Yan committed
81
82
83
84

    names, times, intensities = get_daughterset(ptable, dtable, ds)
    for i in range(len(drlspectrum.lines)):
        drlspectrum.lines[0].remove()
85
86
87
    for i,j in enumerate(intensities):
        drlspectrum.plot(times, j, label=names[i],
                color=(colors[i%len(colors)] / 255))
Yan's avatar
Yan committed
88
89
90
    if len(names) != 0:
        drlspectrum.set_ylim(top=np.amax(intensities)*1.1,
                bottom=np.amax(intensities)*-0.01)
91
    drlspectrum.legend()
Yan's avatar
Yan committed
92
    drlspectrum.figure.canvas.draw()
93

94
95
96
97
98
99
100
101
102
103
104
    count = 0
    for row in range(dtable.rowCount()):
        #print(row)
        print(count)
        if dtable.cellWidget(row, 1).checkState() ==2:
            dtable.item(row,0).setBackground(QtGui.QBrush(
                QtGui.QColor(*colors[count%len(colors)], alpha=50)))
            count += 1
        else:
            dtable.item(row,0).setBackground(QtGui.QBrush())

Yan's avatar
Yan committed
105

106
def getTableItemList(ptable):
107
    ion_list = []
Yan's avatar
Yan committed
108
109
110
111
112
113
114
115
116
117
    for row in range(ptable.rowCount()):
        text = []
        for i in range(3):
            if type(ptable.cellWidget(row, i)) is not type(None):
                frg = ptable.cellWidget(row, i).text()
            else:
                frg = ""
            text.append(frg)
        line = "{} ({}-{})".format(*text)
        ion_list.append(line)
118
119
120
121
    return ion_list


def update_drl(start_mz, end_mz, spectrum, dataset, pname, dname,
Yan's avatar
Yan committed
122
        ptable, dtable, drlspectrum):
Yan's avatar
Yan committed
123
124
    """cares that masses are in order and valid, then refresh tables"""
    for line in start_mz, end_mz:
Yan's avatar
Yan committed
125
126
127
        status = QtGui.QDoubleValidator().validate(line.text(), 0)[0]
        if status != QtGui.QValidator.Acceptable:
            line.setText("0")
Yan's avatar
Yan committed
128

Yan's avatar
Yan committed
129
130
    start = dt.floatize(start_mz.text())
    end = dt.floatize(end_mz.text())
131
132
133

    if start > end:
        start, end = end, start
134
135
136

    if float(0) not in (start, end) and pname.text() is "":
        pname.setText(str(int((start+end)/2)))
137

Yan's avatar
Yan committed
138
139
140
141
142
143
144
145
    ptnames = getTableItemList(ptable)
    for row in range(dtable.rowCount()):
        dtable.item(row,1).setText(ptnames[row])
        index = dtable.cellWidget(row,2).currentIndex()
        dtable.cellWidget(row,2).clear()
        dtable.cellWidget(row,2).addItem("")
        dtable.cellWidget(row,2).addItems(getTableItemList(ptable))
        dtable.cellWidget(row,2).setCurrentIndex(index)
Yan's avatar
Yan committed
146

Yan's avatar
Yan committed
147
148
    update_profile(start, end, spectrum, dataset)
    update_drlspectrum(ptable, dtable, dataset, drlspectrum)
149
150
151


def remove_rows(ptable, dtable):
Yan's avatar
Yan committed
152
    # TODO: maybe nicer selection in future, but this works for now
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
    rows = reversed(list(set(
        map(lambda index: index.row(), ptable.selectedIndexes()))))
    for row in rows:
        dtable.removeRow(row)
        ptable.removeRow(row)
        for i in range(dtable.rowCount()):
            index = dtable.cellWidget(i,2).currentIndex()
            dtable.cellWidget(i,2).clear()
            dtable.cellWidget(i,2).addItem("")
            dtable.cellWidget(i,2).addItems(getTableItemList(ptable))
            if index == row+1:
                dtable.cellWidget(i,2).setCurrentIndex(0)
            elif index > row+1:
                dtable.cellWidget(i,2).setCurrentIndex(index-1)


Yan's avatar
Yan committed
169
def setDoubleCell(table, row, column):
170
171
172
173
174
175
176
177
178
179
180
181
    """populate table cell with float-validated posititve text"""
    table.setCellWidget(row,column,QtWidgets.QLineEdit())
    validator = QtGui.QDoubleValidator()
    validator.setBottom(0)
    table.cellWidget(row,column).setValidator(validator)
    table.cellWidget(row,column).setFrame(False)
    table.cellWidget(row,column).setText("0")
    table.horizontalHeader().setSectionResizeMode(
            column, QtWidgets.QHeaderView.ResizeToContents)
    return table.cellWidget(row,column)


Yan's avatar
Yan committed
182
def add_line(parent_widget, ds, parenttable,
Yan's avatar
Yan committed
183
        daughtertable, drlspectrum):
184
185
186
187
188
189
190
191
192
    """add parent ion to the table"""
    ion_graph = Figure(figsize=(3, 1.5), dpi=100, facecolor="None")
    ionspect = ion_graph.add_subplot(111, facecolor=(1, 1, 1, 0.8),
            position=(-0.01,-0.01,1.02,1.02))
    graph_canvas = FigureCanvas(ion_graph)
    graph_canvas.setStyleSheet("background-color:transparent;")
    graph_canvas.setAutoFillBackground(False)

    newrow = parenttable.rowCount()
193

194
195
196
197
198
199
200
    parenttable.setRowCount(newrow + 1)
    pname = QtWidgets.QLineEdit()
    pname.setFrame(False)
    parenttable.setCellWidget(newrow, 0, pname)
    start_mz = setDoubleCell(parenttable, newrow, 1)
    end_mz = setDoubleCell(parenttable, newrow, 2)
    parenttable.setCellWidget(newrow, 3, graph_canvas)
201
202
203
204
205
    if newrow is not 0:
        for i in range(3):
            parenttable.cellWidget(newrow, i).setText(
                str(dt.floatize(
                    parenttable.cellWidget(newrow-1, i).text())+1))
206

207
    daughtertable.setRowCount(newrow + 1)
Yan's avatar
Yan committed
208
209

    #TODO: decide which box will be used in the final version
Yan's avatar
Yan committed
210
    checkbox = QtWidgets.QCheckBox()
211
212
213
214
    daughtertable.setItem(newrow,0, QtWidgets.QTableWidgetItem())
    daughtertable.item(newrow,0).setFlags(daughtertable.item(newrow,0).flags()
            & ~QtCore.Qt.ItemIsSelectable)
    daughtertable.setCellWidget(newrow, 0, QtWidgets.QCheckBox())
215

216
217
    dname = QtWidgets.QTableWidgetItem()
    dname.setFlags(dname.flags() & ~QtCore.Qt.ItemIsEditable)
Yan's avatar
Yan committed
218
    dname.setTextAlignment(QtCore.Qt.AlignRight)
219
    daughtertable.setItem(newrow, 1, dname)
Yan's avatar
Yan committed
220
    daughtertable.setCellWidget(newrow, 1, checkbox)
221

222
223
224
225
226
    corto = QtWidgets.QComboBox()
    corto.setFrame(False)
    corto.addItem("")
    corto.addItems(getTableItemList(parenttable))
    daughtertable.setCellWidget(newrow, 2, corto)
227

228
    corfact = setDoubleCell(daughtertable, newrow, 3)
229

230
    update_drl(start_mz, end_mz, ionspect, ds, pname, dname, 
Yan's avatar
Yan committed
231
            parenttable, daughtertable, drlspectrum)
232

Yan's avatar
Yan committed
233
234
    pname.editingFinished.connect(lambda: update_drl(
        start_mz, end_mz, ionspect, ds, pname, dname, parenttable,
Yan's avatar
Yan committed
235
        daughtertable, drlspectrum))
236
237
    start_mz.editingFinished.connect(lambda: update_drl(
        start_mz, end_mz, ionspect, ds, pname, dname, parenttable,
Yan's avatar
Yan committed
238
        daughtertable, drlspectrum))
239
240
    end_mz.editingFinished.connect(lambda: update_drl(
        start_mz, end_mz, ionspect, ds, pname, dname, parenttable,
Yan's avatar
Yan committed
241
242
243
        daughtertable, drlspectrum))
    checkbox.stateChanged.connect(lambda: update_drlspectrum(
        parenttable, daughtertable, ds, drlspectrum))
244
245


246
247
248
def iontable(labels, exp_col):
    """creates a table for ions"""
    table = QtWidgets.QTableWidget(columnCount=len(labels))
249
    table.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
250
251
                        QtWidgets.QSizePolicy.Expanding)
    table.setHorizontalHeaderLabels(labels)
252
253
254
255
256
257
258
    table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)

    for n in range(table.columnCount()):
        table.horizontalHeader().setSectionResizeMode(
            n, QtWidgets.QHeaderView.Stretch)
    table.setMinimumSize(600,0)

259
    return table
260
261


Yan's avatar
Yan committed
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
def load_drltables(parent, ptable, dtable, dataset, drlspectrum):
    filename = QtWidgets.QFileDialog.getOpenFileName(
            caption="Load DRL config tables",
            filter="comma-separated values (*.csv)")[0]
    if filename is not '':
        names = []
        start_masses = []
        end_masses = []
        states = []
        corrected_to = []
        corr_factors = []

        with open(filename, 'r') as cfile:
            rawdata = cfile.read().splitlines()
        for i in range(1,len(rawdata)):
            rawline=rawdata[i].split(",")
            if len(rawline) != 6 or int(rawline[3]) not in range(3) \
                    or int(rawline[4]) not in range(len(rawdata)):
                QtWidgets.QMessageBox.warning(
                    parent, "Load DRL config tables",
                    "Config file corrupted on line {},"
                    " cancelling request".format(i+1))
                return
            for j, k in enumerate((names, start_masses, end_masses,
                               states, corrected_to, corr_factors)):
                k.append(rawline[j])
Yan's avatar
Yan committed
288
289
290
        for row in reversed(range(ptable.rowCount())):
            dtable.removeRow(row)
            ptable.removeRow(row)
Yan's avatar
Yan committed
291
292
293
294
295
296
297
298
299
300
301
302
303
        #first populate only parent table
        for i in range(len(names)):
            add_line(parent, dataset, ptable, dtable, drlspectrum)
            print(names[i])
            ptable.cellWidget(i, 0).setText(names[i])
            ptable.cellWidget(i, 1).setText(start_masses[i])
            ptable.cellWidget(i, 2).setText(end_masses[i])
        #and after that daughter table
        for i in range(len(names)):
            dtable.cellWidget(i, 2).setCurrentIndex(
                int(corrected_to[i]))
            dtable.cellWidget(i, 3).setText(corr_factors[i])
            dtable.cellWidget(i, 1).setCheckState(int(states[i]))
Yan's avatar
Yan committed
304
305


Yan's avatar
Yan committed
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
def save_drlconfig(ptable, dtable, parent):
    """safe DRL table layout so it can be summoned when needed"""
    exp_f_name = ft.get_save_filename(
        "Save DRL table layout", "comma-separated values (*.csv)",
        "csv", parent)
    if exp_f_name is not '':
        expf = open(exp_f_name, 'w')
        expf.write("#ion_name, start m/z, end m/z, visible,"
                   "corrected_to, factor\n")
        for row in range(ptable.rowCount()):
            vals = []
            for i in range(3):
                vals.append(ptable.cellWidget(row,i).text())
            vals.append(dtable.cellWidget(row,1).checkState())
            vals.append(dtable.cellWidget(row,2).currentIndex())
            vals.append(dtable.cellWidget(row,3).text())
            #vals = ",".join(map(str, vals))
            expf.write("{}\n".format((",".join(map(str, vals)))))
        expf.close()

Yan's avatar
Yan committed
326

Yan's avatar
Yan committed
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
def export_drlspectrum(parent, fn, ptable, dtable, ds):
    if fn[0] is None:
        QtWidgets.QMessageBox.warning(
            main_window, "Export DRL dataset",
            "Nothing to export, cancelling request")
        return
    names, times, intensities = get_daughterset(ptable, dtable, ds)
    exp_f_name = ft.get_save_filename(
        "Export DRL data", "comma-separated values (*.csv)", "csv", parent)
    if exp_f_name is not '':
        expf = open(exp_f_name, 'w')
        expf.write("times, {}\n".format((",".join(names))))
        for i in range(len(times)):
            dataset = []
            dataset.append(times[i])
            for intensity in intensities:
                dataset.append(intensity[i])
            expf.write("{}\n".format((",".join(map(str, dataset)))))
        expf.close()

Yan's avatar
Yan committed
347

Yan's avatar
Yan committed
348
def main_window(parent, ds, filename, cache):
349
    """constructs a dialog window"""
Yan's avatar
Yan committed
350
    def saveonclose(window, event, cache,pt,dt,canvas):
Yan's avatar
Yan committed
351
        cache[0], cache[1], cache[2] = pt, dt, canvas
Yan's avatar
Yan committed
352
        QtWidgets.QMainWindow.closeEvent(window, event)
Yan's avatar
Yan committed
353

Yan's avatar
Yan committed
354
    main_window = QtWidgets.QMainWindow(
Yan's avatar
Yan committed
355
        parent, windowTitle='Delayed reactant labelling')
Yan's avatar
Yan committed
356
357
358
359
360
    dial_widget = QtWidgets.QWidget(main_window)
    main_window.setCentralWidget(dial_widget)

    main_window.closeEvent = lambda event: saveonclose(
        main_window, event, cache, pt, dt, graph_canvas)
Yan's avatar
Yan committed
361

Yan's avatar
Yan committed
362
363
    dial_graph = Figure(figsize=(5, 2), dpi=100, facecolor="None")
    chromplot = dial_graph.add_subplot(111, facecolor=(1, 1, 1, 0.8))
Yan's avatar
Yan committed
364
365
366
    graph_canvas = FigureCanvas(dial_graph)
    graph_canvas.setStyleSheet("background-color:transparent;")
    graph_canvas.setAutoFillBackground(False)
Yan's avatar
Yan committed
367
368
369
370
371
372
    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, graphlabels)

Yan's avatar
Yan committed
373

374
375
376
377
    drl_load = QtWidgets.QPushButton("&Load")
    drl_save = QtWidgets.QPushButton("&Save")
    drl_export = QtWidgets.QPushButton("&Export")
    close = QtWidgets.QPushButton("&Close")
378
379
    close.clicked.connect(dial_widget.close)

Yan's avatar
Yan committed
380
381
382
    btn_add = QtWidgets.QPushButton("&Add")
    btn_rem = QtWidgets.QPushButton("Remove")

383
384
    # pt = parenttable
    # dt = daughtertable
Yan's avatar
Yan committed
385
    if cache == [None, None, None]:
Yan's avatar
Yan committed
386
387
        dt = iontable(["","Name", "corrected to", "factor"], 2)
        dt.horizontalHeader().setSectionResizeMode(
388
            0, QtWidgets.QHeaderView.ResizeToContents)
Yan's avatar
Yan committed
389
        dt.horizontalHeader().setSectionResizeMode(
390
391
            3, QtWidgets.QHeaderView.Fixed)

Yan's avatar
Yan committed
392
        pt = iontable(["Name", "start (m/z)", "end (m/z)", "profile"], 2)
393
        add_line(dial_widget, ds, pt, dt, chromplot)
Yan's avatar
Yan committed
394
395
396
    else:
        pt = cache[0]
        dt = cache[1]
Yan's avatar
Yan committed
397
        graph_canvas = cache[2]
398
399

    btn_add.clicked.connect(lambda: add_line(
Yan's avatar
Yan committed
400
        dial_widget, ds, pt, dt, chromplot))
401
    btn_rem.clicked.connect(lambda: remove_rows(pt,dt))
Yan's avatar
Yan committed
402
403
    drl_load.clicked.connect(lambda: load_drltables(
        dial_widget, pt, dt, ds, chromplot))
Yan's avatar
Yan committed
404
405
    drl_save.clicked.connect(lambda: save_drlconfig(
        pt, dt, dial_widget))
Yan's avatar
Yan committed
406
407
    drl_export.clicked.connect(lambda: export_drlspectrum(
        dial_widget, filename, pt, dt, ds))
Yan's avatar
Yan committed
408

409

Yan's avatar
Yan committed
410
411
412
    main_layout = QtWidgets.QVBoxLayout(dial_widget)
    sub_layout = QtWidgets.QHBoxLayout()
    tablelayout = QtWidgets.QVBoxLayout()
Yan's avatar
Yan committed
413
    pt_butlayout = QtWidgets.QHBoxLayout()
Yan's avatar
Yan committed
414
    main_butlayout = QtWidgets.QHBoxLayout()
Yan's avatar
Yan committed
415

Yan's avatar
Yan committed
416
417
418
419
    pt_butlayout.addWidget(btn_add)
    pt_butlayout.addWidget(btn_rem)
    pt_butlayout.addStretch(0)

420
421
    main_layout.addLayout(sub_layout)
    main_layout.addWidget(HBar())
Yan's avatar
Yan committed
422
    main_layout.addLayout(main_butlayout)
423

Yan's avatar
Yan committed
424
425
426
427
    main_butlayout.addWidget(drl_load)
    main_butlayout.addWidget(drl_save)
    main_butlayout.addStretch(1)
    main_butlayout.addWidget(drl_export)
428
    main_butlayout.addWidget(close)
Yan's avatar
Yan committed
429

430
    sub_layout.addWidget(graph_canvas, stretch=1)
Yan's avatar
Yan committed
431
    sub_layout.addLayout(tablelayout)
432

Yan's avatar
Yan committed
433
434
435
436
437
    tablelayout.addWidget(QtWidgets.QLabel("Raw ions table:"))
    tablelayout.addWidget(pt)
    tablelayout.addLayout(pt_butlayout)
    tablelayout.addWidget(QtWidgets.QLabel("Corrected ions table:"))
    tablelayout.addWidget(dt)
438

Yan's avatar
Yan committed
439
    main_window.show()