Unite spectrum variables and objects into one class

prasopes/__main__.py

@@ -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

@@ -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

@@ -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

@@ -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(msx, msy, augCanvas.spectplot, augCanvas.ms,