drltools.py 13 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
80
81
82
83
84
85
86
87
88
89
            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

    names, times, intensities = get_daughterset(ptable, dtable, ds)
    for i in range(len(drlspectrum.lines)):
        drlspectrum.lines[0].remove()
    for i in intensities:
        drlspectrum.plot(times, i)
    if len(names) != 0:
        drlspectrum.set_ylim(top=np.amax(intensities)*1.1,
                bottom=np.amax(intensities)*-0.01)
    drlspectrum.figure.canvas.draw()
90

Yan's avatar
Yan committed
91

92
def getTableItemList(ptable):
93
    ion_list = []
Yan's avatar
Yan committed
94
95
96
97
98
99
100
101
102
103
    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)
104
105
106
107
    return ion_list


def update_drl(start_mz, end_mz, spectrum, dataset, pname, dname,
Yan's avatar
Yan committed
108
        ptable, dtable, drlspectrum):
Yan's avatar
Yan committed
109
110
    """cares that masses are in order and valid, then refresh tables"""
    for line in start_mz, end_mz:
Yan's avatar
Yan committed
111
112
113
        status = QtGui.QDoubleValidator().validate(line.text(), 0)[0]
        if status != QtGui.QValidator.Acceptable:
            line.setText("0")
Yan's avatar
Yan committed
114

Yan's avatar
Yan committed
115
116
    start = dt.floatize(start_mz.text())
    end = dt.floatize(end_mz.text())
117
118
119
120
121
122

    if start > end:
        start, end = end, start
        start_mz.setText(str(start))
        end_mz.setText(str(end))

Yan's avatar
Yan committed
123
124
125
126
127
128
129
130
    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
131

Yan's avatar
Yan committed
132
133
    update_profile(start, end, spectrum, dataset)
    update_drlspectrum(ptable, dtable, dataset, drlspectrum)
134
135
136


def remove_rows(ptable, dtable):
Yan's avatar
Yan committed
137
    # TODO: maybe nicer selection in future, but this works for now
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
    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)


def setDoubleCell(table,row,column):
    """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
167
168
def add_line(parent_widget, mass_selector, spectrum, ds, parenttable,
        daughtertable, drlspectrum):
169
170
171
172
173
174
175
176
177
    """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()
178

179
180
181
182
183
184
185
    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)
186

187
    daughtertable.setRowCount(newrow + 1)
Yan's avatar
Yan committed
188
189

    #TODO: decide which box will be used in the final version
Yan's avatar
Yan committed
190
    checkbox = QtWidgets.QCheckBox()
191
192
193
194
    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())
195

196
197
    dname = QtWidgets.QTableWidgetItem()
    dname.setFlags(dname.flags() & ~QtCore.Qt.ItemIsEditable)
Yan's avatar
Yan committed
198
    dname.setTextAlignment(QtCore.Qt.AlignRight)
199
    daughtertable.setItem(newrow, 1, dname)
Yan's avatar
Yan committed
200
    daughtertable.setCellWidget(newrow, 1, checkbox)
201

202
203
204
205
206
    corto = QtWidgets.QComboBox()
    corto.setFrame(False)
    corto.addItem("")
    corto.addItems(getTableItemList(parenttable))
    daughtertable.setCellWidget(newrow, 2, corto)
207

208
    corfact = setDoubleCell(daughtertable, newrow, 3)
209

210
    update_drl(start_mz, end_mz, ionspect, ds, pname, dname, 
Yan's avatar
Yan committed
211
            parenttable, daughtertable, drlspectrum)
212

Yan's avatar
Yan committed
213
214
    pname.editingFinished.connect(lambda: update_drl(
        start_mz, end_mz, ionspect, ds, pname, dname, parenttable,
Yan's avatar
Yan committed
215
        daughtertable, drlspectrum))
216
217
    start_mz.editingFinished.connect(lambda: update_drl(
        start_mz, end_mz, ionspect, ds, pname, dname, parenttable,
Yan's avatar
Yan committed
218
        daughtertable, drlspectrum))
219
220
    end_mz.editingFinished.connect(lambda: update_drl(
        start_mz, end_mz, ionspect, ds, pname, dname, parenttable,
Yan's avatar
Yan committed
221
222
223
        daughtertable, drlspectrum))
    checkbox.stateChanged.connect(lambda: update_drlspectrum(
        parenttable, daughtertable, ds, drlspectrum))
224
225


226
227
228
def iontable(labels, exp_col):
    """creates a table for ions"""
    table = QtWidgets.QTableWidget(columnCount=len(labels))
229
    table.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
230
231
                        QtWidgets.QSizePolicy.Expanding)
    table.setHorizontalHeaderLabels(labels)
232
233
234
235
236
237
238
    table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)

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

239
    return table
240
241


Yan's avatar
Yan committed
242
243
244
245
246
247
248
249
def load_drlconfig(ptable, dtable):
    #will be substituted with something that can vwork in future
    if 0 == 1:
        for row in reversed(range(ptable.rowCount())):
            dtable.removeRow(row)
            ptable.removeRow(row)


Yan's avatar
Yan committed
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
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
270
271


Yan's avatar
Yan committed
272
def dialog(parent, ds, filename, mass_selector, spectrum, cache):
273
    """constructs a dialog window"""
274

Yan's avatar
Yan committed
275
276
    def savecache(cache,pt,dt,canvas):
        cache[0], cache[1], cache[2] = pt, dt, canvas
Yan's avatar
Yan committed
277

Yan's avatar
Yan committed
278
279
    dial_widget = QtWidgets.QDialog(
        parent, windowTitle='Delayed reactant labelling')
Yan's avatar
Yan committed
280

Yan's avatar
Yan committed
281
282
    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
283
284
285
    graph_canvas = FigureCanvas(dial_graph)
    graph_canvas.setStyleSheet("background-color:transparent;")
    graph_canvas.setAutoFillBackground(False)
Yan's avatar
Yan committed
286
287
288
289
290
291
    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
292

293
294
295
296
    drl_load = QtWidgets.QPushButton("&Load")
    drl_save = QtWidgets.QPushButton("&Save")
    drl_export = QtWidgets.QPushButton("&Export")
    close = QtWidgets.QPushButton("&Close")
297
298
    close.clicked.connect(dial_widget.close)

Yan's avatar
Yan committed
299
300
301
    btn_add = QtWidgets.QPushButton("&Add")
    btn_rem = QtWidgets.QPushButton("Remove")

302
303
    # pt = parenttable
    # dt = daughtertable
Yan's avatar
Yan committed
304
    if cache == [None, None, None]:
Yan's avatar
Yan committed
305
306
        dt = iontable(["","Name", "corrected to", "factor"], 2)
        dt.horizontalHeader().setSectionResizeMode(
307
            0, QtWidgets.QHeaderView.ResizeToContents)
Yan's avatar
Yan committed
308
        dt.horizontalHeader().setSectionResizeMode(
309
310
            3, QtWidgets.QHeaderView.Fixed)

Yan's avatar
Yan committed
311
312
        pt = iontable(["Name", "start (m/z)", "end (m/z)", "profile"], 2)
        for i in range(5):
Yan's avatar
Yan committed
313
314
            add_line(dial_widget, mass_selector, spectrum, ds, pt, dt,
                    chromplot)
Yan's avatar
Yan committed
315
316
317
    else:
        pt = cache[0]
        dt = cache[1]
Yan's avatar
Yan committed
318
        graph_canvas = cache[2]
319
320

    btn_add.clicked.connect(lambda: add_line(
Yan's avatar
Yan committed
321
        dial_widget, mass_selector, spectrum, ds, pt, dt, chromplot))
322
    btn_rem.clicked.connect(lambda: remove_rows(pt,dt))
Yan's avatar
Yan committed
323
    drl_load.clicked.connect(lambda: load_drlconfig(pt, dt))
Yan's avatar
Yan committed
324
325
326
327
    drl_save.clicked.connect(lambda: save_drlconfig(
        pt, dt, dial_widget))
    dial_widget.finished.connect(lambda: savecache(
        cache, pt, dt, graph_canvas))
328

Yan's avatar
Yan committed
329
330
331
    main_layout = QtWidgets.QVBoxLayout(dial_widget)
    sub_layout = QtWidgets.QHBoxLayout()
    tablelayout = QtWidgets.QVBoxLayout()
Yan's avatar
Yan committed
332
    pt_butlayout = QtWidgets.QHBoxLayout()
Yan's avatar
Yan committed
333
    main_butlayout = QtWidgets.QHBoxLayout()
Yan's avatar
Yan committed
334

Yan's avatar
Yan committed
335
336
337
338
    pt_butlayout.addWidget(btn_add)
    pt_butlayout.addWidget(btn_rem)
    pt_butlayout.addStretch(0)

339
340
    main_layout.addLayout(sub_layout)
    main_layout.addWidget(HBar())
Yan's avatar
Yan committed
341
    main_layout.addLayout(main_butlayout)
342

Yan's avatar
Yan committed
343
344
345
346
    main_butlayout.addWidget(drl_load)
    main_butlayout.addWidget(drl_save)
    main_butlayout.addStretch(1)
    main_butlayout.addWidget(drl_export)
347
    main_butlayout.addWidget(close)
Yan's avatar
Yan committed
348

349
    sub_layout.addWidget(graph_canvas, stretch=1)
Yan's avatar
Yan committed
350
    sub_layout.addLayout(tablelayout)
351

Yan's avatar
Yan committed
352
353
354
355
356
    tablelayout.addWidget(QtWidgets.QLabel("Raw ions table:"))
    tablelayout.addWidget(pt)
    tablelayout.addLayout(pt_butlayout)
    tablelayout.addWidget(QtWidgets.QLabel("Corrected ions table:"))
    tablelayout.addWidget(dt)
357

Yan's avatar
Yan committed
358
    dial_widget.show()