Code unification - mobtools, msonmobtools

* removed err from last commit
* unified mobility routines
* a bit spaghetti code at the moment

prasopes/__main__.py

@@ -22,7 +22,7 @@ import prasopes.imagetools as imgt
 import prasopes.zcetools as zce
 import prasopes.docks as docks
 import prasopes.datasets as datasets
-import prasopes.mobtools as mt
+import prasopes.mobtools_gui as mtg
 import prasopes.tangoicons
 import sys
 import logging
@@ -350,7 +350,7 @@ def main():
     tofact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
         "applications-utilities"), "&MOB...", None)
     tofact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_M)
-    tofact.triggered.connect(lambda: mt.main_window(
+    tofact.triggered.connect(lambda: mtg.main_window(
         main_window, augCanvas, update))
     aboutact = QtWidgets.QAction("&About Prasopes", None)
     aboutact.triggered.connect(lambda: about(main_window))

prasopes/drltools.py

@@ -24,8 +24,8 @@ def floatize(table, row, column, nonneg=True):
 
 
 def get_subargs(tab, row, masses, col1, col2):
-    startm = drl.floatize(tab, row, col1) - (drl.floatize(tab, row, col2) / 2)
-    endm = drl.floatize(tab, row, col1) + (drl.floatize(tab, row, col2) / 2)
+    startm = floatize(tab, row, col1) - (floatize(tab, row, col2) / 2)
+    endm = floatize(tab, row, col1) + (floatize(tab, row, col2) / 2)
     massargs = dt.argsubselect(masses, startm, endm)
     return massargs
 

prasopes/mobtools.py

@@ -13,7 +13,7 @@ import prasopes.filetools as ft
 import prasopes.config as cf
 import prasopes.drltools as drl
 import prasopes.imagetools as imgt
-import prasopes.msonmobtools as mmt
+import prasopes.msonmobtools_gui as mmtg
 import os.path
 import logging
 matplotlib.use("Qt5Agg")
@@ -23,44 +23,17 @@ logger = logging.getLogger('tofLogger')
 settings = cf.settings()
 
 
-def update_profile(table, row, dataset):
-    """parent table profile spectrum updating procedure"""
-    logger.debug("updating parent table row {} profile".format(row))
-    # Dont do anything to graph when the spectrum is not populated
-    if not dataset or isinstance(dataset, ds.ThermoRawDataset):
-        return
-    spectrum = table.cellWidget(row, 5).figure.get_axes()[0]
-    spectrum.clear()
-    limits = []
-    spectra = dataset.get_spectra(*[drl.floatize(table, row, i)
-                                    for i in (1, 2)])
-    for i, spectxy in enumerate(spectra):
-        massargs = drl.get_subargs(table, row, spectxy[0], 3, 4)
-        spectrum.plot(spectxy[0], spectxy[1], ':', color='gray')
-        spectrum.plot(spectxy[0][massargs], spectxy[1][massargs],
-                      color=gt.colors[i % len(gt.colors)]/255)
-        limits.append((spectxy[0][massargs[[0, -1]]],
-                       max(spectxy[1][massargs])))
-    widest = np.argmax([abs(lim[0][1]-lim[0][0]) for lim in limits])
-    xmin, xmax = limits[widest][0]
-    xex = max((xmax-xmin)*0.25, 0.02)
-    spectrum.set_xlim(xmin-xex, xmax+xex)
-    ymax = max(*[lim[1] for lim in limits], 1)
-    spectrum.set_ylim(ymax*-0.1, ymax*1.2)
-    spectrum.figure.canvas.draw()
-
 
-def ionstable_changed(row, col, ds, table):
+def ionstable_changed(row, col, dsfunc, table):
     if col in (1, 2, 3, 4):
-        update_profile(table, row, ds)
+        update_profile(table, row, dsfunc)
     table.blockSignals(True)
     table.item(row, 0).setBackground(QtGui.QBrush(
         QtGui.QColor(*gt.colors[row % len(gt.colors)], alpha=50)))
     table.blockSignals(False)
 
 
-def pop_dial(augCanvas, dialspect, ionstable, labels):
-    ds = augCanvas.ds
+def pop_dial(dialspect, ionstable, labels, getfnc):
     dialspect.clear()
     gt.pop_plot([], [], dialspect, labels)
     for row in range(ionstable.rowCount()):
@@ -70,7 +43,7 @@ def pop_dial(augCanvas, dialspect, ionstable, labels):
         endm = drl.floatize(ionstable, row, 3)\
             + (drl.floatize(ionstable, row, 4) / 2)
         [tstart, tend] = [drl.floatize(ionstable, row, i) for i in (1, 2)]
-        spectrum = ds.get_mobilogram(startm, endm, tstart, tend)
+        spectrum = getfnc(startm, endm, tstart, tend)
         dialspect.plot(spectrum[0], spectrum[1], label=name,
                        color=(gt.colors[row % len(gt.colors)] / 255))
     if ionstable.rowCount():
@@ -81,7 +54,7 @@ def pop_dial(augCanvas, dialspect, ionstable, labels):
     return
 
 
-def add_row(ds, dialspect, ionstable):
+def add_row(dsfunc, dialspect, ionstable):
     """add parent ion to the table"""
     logger.debug("adding line")
     newrow = ionstable.rowCount()
@@ -106,7 +79,7 @@ def add_row(ds, dialspect, ionstable):
     ionstable.setCellWidget(newrow, 5, graph_canvas)
 
     ionstable.blockSignals(False)
-    ionstable_changed(newrow, 1, ds, ionstable)
+    ionstable_changed(newrow, 1, dsfunc, ionstable)
     return
 
 
@@ -119,96 +92,27 @@ def remove_rows(ionstable, rows=None):
     return
 
 
-def export_dial(augCanvas, grph):
-    """exports the reactivity into the .dat file format"""
-    if not augCanvas.ds or isinstance(augCanvas.ds, ds.ThermoRawDataset):
-        QtWidgets.QMessageBox.warning(
-            None, "Export spectrum",
-            "Nothing to export, cancelling request")
-        return
-    exp_f_name = ft.get_save_filename(
-        "Export spectrum", "dat table (*.dat)", "dat", None)
-    if exp_f_name != '':
-        names = ["1/K_0", "intensity"]
-        units = ["Vs/cm^2", ""]
-        description = os.path.basename(augCanvas.ds.filename) + " " +\
-            " -- ".join([line._label for line in grph.get_lines()])
-        expf = open(exp_f_name, 'w')
-        expf.write(dt.specttostr(grph, " ", names, units, description))
-        expf.close
-
-
-def main_window(parent, augCanvas, update_signal):
-    reactlabels = dict(name="", xlabel="$1/K_0 (Vs/cm^2)\ \\it→$",
-                       ylabel="$Intensity\ \\it→$", annotation=[], texts=[],
-                       ancx=5, ancy=3)
-    cache = augCanvas.tofcache
-
-    def onclose(widget, event, ionstable, canvas, cache, update_fnc):
-        logger.debug("custom close routine called")
-        cache[0], cache[1] = ionstable, canvas
-        update_signal.signal.disconnect(update_fnc)
-        QtWidgets.QDialog.closeEvent(widget, event)
-
-    def update_fnc():
-        pop_dial(augCanvas, dialspect, ionstable, reactlabels)
-
-    dial_widget = QtWidgets.QDialog(
-            parent, windowTitle='Mobilogram')
-    dial_widget.closeEvent = lambda event: onclose(
-        dial_widget, event, ionstable, graph_canvas, cache, update_fnc)
-    update_signal.signal.connect(update_fnc)
-
-    if cache == [None, None]:
-        dial_graph = Figure(figsize=(5, 2), dpi=100, facecolor="None",
-                            constrained_layout=True)
-        dialspect = 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)
-
-        gt.zoom_factory(dialspect, 1.15, reactlabels)
-        gt.pan_factory(dialspect, reactlabels)
-
-        ionstable = dt.table(["Name", "Start time (min)", "End time (min)",
-                              "Mass (m/z)", "Peak width", "Profile"])
-    else:
-        ionstable = cache[0]
-        graph_canvas = cache[1]
-        dialspect = graph_canvas.figure.axes[0]
-
-    ionstable.itemChanged.connect(lambda item: ionstable_changed(
-        item.row(), item.column(), augCanvas.ds, ionstable))
-
-    updatebtn = QtWidgets.QPushButton("Update")
-    updatebtn.clicked.connect(lambda: update_fnc())
-
-    addbtn = QtWidgets.QPushButton("Add")
-    addbtn.clicked.connect(lambda: add_row(
-        augCanvas.ds, dialspect, ionstable))
-    rmbtn = QtWidgets.QPushButton("Remove")
-    rmbtn.clicked.connect(lambda: remove_rows(ionstable))
-
-    mobbtn = QtWidgets.QPushButton("mobMZ")
-    mobbtn.clicked.connect(lambda: mmt.main_window(
-        parent, augCanvas, update_signal))
-    expbtn = QtWidgets.QPushButton("Export")
-    expbtn.clicked.connect(lambda: export_dial(
-        augCanvas, dialspect))
-
-    buttlayout = QtWidgets.QHBoxLayout()
-    buttlayout.addWidget(updatebtn)
-    buttlayout.addStretch()
-    buttlayout.addWidget(addbtn)
-    buttlayout.addWidget(rmbtn)
-    buttlayout.addStretch()
-    buttlayout.addWidget(mobbtn)
-    buttlayout.addWidget(expbtn)
-
-    dial_layout = QtWidgets.QVBoxLayout(dial_widget)
-    dial_layout.addWidget(graph_canvas, stretch=1)
-    dial_layout.addWidget(ionstable)
-    dial_layout.addLayout(buttlayout)
-    dial_widget.setFocus()
-    dial_widget.show()
-    update_fnc()
+def update_profile(table, row, dsfunc):
+    """parent table profile spectrum updating procedure"""
+    logger.debug("updating parent table row {} profile".format(row))
+    # Dont do anything to graph when the spectrum is not populated
+    """if not dataset or isinstance(dataset, ds.ThermoRawDataset):
+        return"""
+    spectrum = table.cellWidget(row, 5).figure.get_axes()[0]
+    spectrum.clear()
+    limits = []
+    spectra = dsfunc(*[drl.floatize(table, row, i) for i in (1, 2)])
+    for i, spectxy in enumerate(spectra):
+        massargs = drl.get_subargs(table, row, spectxy[0], 3, 4)
+        spectrum.plot(spectxy[0], spectxy[1], ':', color='gray')
+        spectrum.plot(spectxy[0][massargs], spectxy[1][massargs],
+                      color=gt.colors[i % len(gt.colors)]/255)
+        limits.append((spectxy[0][massargs[[0, -1]]],
+                       max(spectxy[1][massargs])))
+    widest = np.argmax([abs(lim[0][1]-lim[0][0]) for lim in limits])
+    xmin, xmax = limits[widest][0]
+    xex = max((xmax-xmin)*0.25, 0.02)
+    spectrum.set_xlim(xmin-xex, xmax+xex)
+    ymax = max(*[lim[1] for lim in limits], 1)
+    spectrum.set_ylim(ymax*-0.1, ymax*1.2)
+    spectrum.figure.canvas.draw()

prasopes/mobtools_gui.py

+#!/usr/bin/env python3
+from matplotlib.backends.backend_qt5agg import\
+        FigureCanvasQTAgg as FigureCanvas
+from matplotlib.figure import Figure
+from PyQt5 import QtWidgets
+from PyQt5 import QtGui
+import matplotlib
+import numpy as np
+import prasopes.datasets as ds
+import prasopes.datatools as dt
+import prasopes.graphtools as gt
+import prasopes.filetools as ft
+import prasopes.config as cf
+import prasopes.drltools as drl
+import prasopes.imagetools as imgt
+import prasopes.msonmobtools_gui as mmtg
+import prasopes.mobtools as mt
+import os.path
+import logging
+matplotlib.use("Qt5Agg")
+
+
+logger = logging.getLogger('tofLogger')
+settings = cf.settings()
+
+
+def export_dial(augCanvas, grph):
+    """exports the reactivity into the .dat file format"""
+    if not augCanvas.ds or isinstance(augCanvas.ds, ds.ThermoRawDataset):
+        QtWidgets.QMessageBox.warning(
+            None, "Export spectrum",
+            "Nothing to export, cancelling request")
+        return
+    exp_f_name = ft.get_save_filename(
+        "Export spectrum", "dat table (*.dat)", "dat", None)
+    if exp_f_name != '':
+        names = ["1/K_0", "intensity"]
+        units = ["Vs/cm^2", ""]
+        description = os.path.basename(augCanvas.ds.filename) + " " +\
+            " -- ".join([line._label for line in grph.get_lines()])
+        expf = open(exp_f_name, 'w')
+        expf.write(dt.specttostr(grph, " ", names, units, description))
+        expf.close
+
+
+def main_window(parent, augCanvas, update_signal):
+    reactlabels = dict(name="", xlabel="$1/K_0 (Vs/cm^2)\ \\it→$",
+                       ylabel="$Intensity\ \\it→$", annotation=[], texts=[],
+                       ancx=5, ancy=3)
+    cache = augCanvas.tofcache
+
+    def onclose(widget, event, ionstable, canvas, cache, update_fnc):
+        logger.debug("custom close routine called")
+        cache[0], cache[1] = ionstable, canvas
+        update_signal.signal.disconnect(update_fnc)
+        QtWidgets.QDialog.closeEvent(widget, event)
+
+    def update_fnc():
+        mt.pop_dial(dialspect, ionstable, reactlabels,
+                    augCanvas.ds.get_mobilogram)
+
+    dial_widget = QtWidgets.QDialog(
+            parent, windowTitle='Mobilogram')
+    dial_widget.closeEvent = lambda event: onclose(
+        dial_widget, event, ionstable, graph_canvas, cache, update_fnc)
+    update_signal.signal.connect(update_fnc)
+
+    if cache == [None, None]:
+        dial_graph = Figure(figsize=(5, 2), dpi=100, facecolor="None",
+                            constrained_layout=True)
+        dialspect = 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)
+
+        gt.zoom_factory(dialspect, 1.15, reactlabels)
+        gt.pan_factory(dialspect, reactlabels)
+
+        ionstable = dt.table(["Name", "Start time (min)", "End time (min)",
+                              "Mass (m/z)", "Peak width", "Profile"])
+    else:
+        ionstable = cache[0]
+        graph_canvas = cache[1]
+        dialspect = graph_canvas.figure.axes[0]
+
+    ionstable.itemChanged.connect(lambda item: mt.ionstable_changed(
+        item.row(), item.column(), augCanvas.ds.get_spectra, ionstable))
+
+    updatebtn = QtWidgets.QPushButton("Update")
+    updatebtn.clicked.connect(lambda: update_fnc())
+
+    addbtn = QtWidgets.QPushButton("Add")
+    addbtn.clicked.connect(lambda: mt.add_row(
+        augCanvas.ds.get_spectra, dialspect, ionstable))
+    rmbtn = QtWidgets.QPushButton("Remove")
+    rmbtn.clicked.connect(lambda: mt.remove_rows(ionstable))
+
+    mobbtn = QtWidgets.QPushButton("mobMZ")
+    mobbtn.clicked.connect(lambda: mmtg.main_window(
+        parent, augCanvas, update_signal))
+    expbtn = QtWidgets.QPushButton("Export")
+    expbtn.clicked.connect(lambda: export_dial(
+        augCanvas, dialspect))
+
+    buttlayout = QtWidgets.QHBoxLayout()
+    buttlayout.addWidget(updatebtn)
+    buttlayout.addStretch()
+    buttlayout.addWidget(addbtn)
+    buttlayout.addWidget(rmbtn)
+    buttlayout.addStretch()
+    buttlayout.addWidget(mobbtn)
+    buttlayout.addWidget(expbtn)
+
+    dial_layout = QtWidgets.QVBoxLayout(dial_widget)
+    dial_layout.addWidget(graph_canvas, stretch=1)
+    dial_layout.addWidget(ionstable)
+    dial_layout.addLayout(buttlayout)
+    dial_widget.setFocus()
+    dial_widget.show()
+    update_fnc()

prasopes/msonmobtools.py → prasopes/msonmobtools_gui.py

@@ -13,6 +13,7 @@ import prasopes.filetools as ft
 import prasopes.config as cf
 import prasopes.drltools as drl
 import prasopes.imagetools as imgt
+import prasopes.mobtools as mt
 import os.path
 import logging
 matplotlib.use("Qt5Agg")
@@ -22,102 +23,6 @@ logger = logging.getLogger('msonmobLogger')
 settings = cf.settings()
 
 
-def update_profile(table, row, dataset):
-    """parent table profile spectrum updating procedure"""
-    logger.debug("updating parent table row {} profile".format(row))
-    # Dont do anything to graph when the spectrum is not populated
-    if not dataset or isinstance(dataset, ds.ThermoRawDataset):
-        return
-    spectrum = table.cellWidget(row, 5).figure.get_axes()[0]
-    spectrum.clear()
-    limits = []
-    spectra = dataset.get_mobspectra(*[drl.floatize(table, row, i)
-                                    for i in (1, 2)])
-    for i, spectxy in enumerate(spectra):
-        massargs = drl.get_subargs(table, row, spectxy[0], 3, 4)
-        spectrum.plot(spectxy[0], spectxy[1], ':', color='gray')
-        spectrum.plot(spectxy[0][massargs], spectxy[1][massargs],
-                      color=gt.colors[i % len(gt.colors)]/255)
-        limits.append((spectxy[0][massargs[[0, -1]]],
-                       max(spectxy[1][massargs])))
-    widest = np.argmax([abs(lim[0][1]-lim[0][0]) for lim in limits])
-    xmin, xmax = limits[widest][0]
-    xex = max((xmax-xmin)*0.25, 0.02)
-    spectrum.set_xlim(xmin-xex, xmax+xex)
-    ymax = max(*[lim[1] for lim in limits], 1)
-    spectrum.set_ylim(ymax*-0.1, ymax*1.2)
-    spectrum.figure.canvas.draw()
-
-
-def ionstable_changed(row, col, ds, table):
-    if col in (1, 2, 3, 4):
-        update_profile(table, row, ds)
-    table.blockSignals(True)
-    table.item(row, 0).setBackground(QtGui.QBrush(
-        QtGui.QColor(*gt.colors[row % len(gt.colors)], alpha=50)))
-    table.blockSignals(False)
-
-
-def pop_dial(augCanvas, dialspect, ionstable, labels):
-    ds = augCanvas.ds
-    dialspect.clear()
-    gt.pop_plot([], [], dialspect, labels)
-    for row in range(ionstable.rowCount()):
-        name = ionstable.item(row, 0).text()
-        startmob = drl.floatize(ionstable, row, 3)\
-            - (drl.floatize(ionstable, row, 4) / 2)
-        endmob = drl.floatize(ionstable, row, 3)\
-            + (drl.floatize(ionstable, row, 4) / 2)
-        [tstart, tend] = [drl.floatize(ionstable, row, i) for i in (1, 2)]
-        spectrum = ds.get_ms_onmob(startmob, endmob, tstart, tend)
-        dialspect.plot(spectrum[0], spectrum[1], label=name,
-                       color=(gt.colors[row % len(gt.colors)] / 255))
-    if ionstable.rowCount():
-        dialspect.autoscale(True)
-        dialspect.legend(loc=2)
-    gt.ann_spec(dialspect, labels)
-    dialspect.figure.canvas.draw()
-    return
-
-
-def add_row(ds, dialspect, ionstable):
-    """add parent ion to the table"""
-    logger.debug("adding line")
-    newrow = ionstable.rowCount()
-
-    ionstable.blockSignals(True)
-
-    ionstable.setRowCount(newrow + 1)
-    for i in range(5):
-        ionstable.setItem(newrow, i, QtWidgets.QTableWidgetItem())
-        if newrow != 0:
-            val = drl.floatize(ionstable, newrow-1, i)
-            if i not in (1, 2, 4):
-                val = val+1
-            ionstable.item(newrow, i).setText(str(val))
-
-    ion_graph = Figure(figsize=(3, 1.5), dpi=100, facecolor="None")
-    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)
-    ionstable.setCellWidget(newrow, 5, graph_canvas)
-
-    ionstable.blockSignals(False)
-    ionstable_changed(newrow, 1, ds, ionstable)
-    return
-
-
-def remove_rows(ionstable, rows=None):
-    logger.info("remowing rows")
-    if not rows:
-        rows = reversed(list(set(
-            map(lambda x: x.row(), ionstable.selectedIndexes()))))
-    [ionstable.removeRow(row) for row in rows]
-    return
-
-
 def export_dial(augCanvas, grph):
     """exports the reactivity into the .dat file format"""
     if not augCanvas.ds or isinstance(augCanvas.ds, ds.ThermoRawDataset):
@@ -150,7 +55,8 @@ def main_window(parent, augCanvas, update_signal):
         QtWidgets.QDialog.closeEvent(widget, event)
 
     def update_fnc():
-        pop_dial(augCanvas, dialspect, ionstable, reactlabels)
+        mt.pop_dial(dialspect, ionstable, reactlabels,
+                    augCanvas.ds.get_ms_onmob)
 
     dial_widget = QtWidgets.QDialog(
             parent, windowTitle='m/z - mobility')
@@ -176,17 +82,17 @@ def main_window(parent, augCanvas, update_signal):
         graph_canvas = cache[1]
         dialspect = graph_canvas.figure.axes[0]
 
-    ionstable.itemChanged.connect(lambda item: ionstable_changed(
-        item.row(), item.column(), augCanvas.ds, ionstable))
+    ionstable.itemChanged.connect(lambda item: mt.ionstable_changed(
+        item.row(), item.column(), augCanvas.ds.get_mobspectra, ionstable))
 
     updatebtn = QtWidgets.QPushButton("Update")
     updatebtn.clicked.connect(lambda: update_fnc())
 
     addbtn = QtWidgets.QPushButton("Add")
-    addbtn.clicked.connect(lambda: add_row(
-        augCanvas.ds, dialspect, ionstable))
+    addbtn.clicked.connect(lambda: mt.add_row(
+        augCanvas.ds.get_mobspectra, dialspect, ionstable))
     rmbtn = QtWidgets.QPushButton("Remove")
-    rmbtn.clicked.connect(lambda: remove_rows(ionstable))
+    rmbtn.clicked.connect(lambda: mt.remove_rows(ionstable))
 
     expbtn = QtWidgets.QPushButton("Export")
     expbtn.clicked.connect(lambda: export_dial(