Parameters log pt1

* Experimental parameters support for TSQ, without time subselection
* fixed file loading exception handling

prasopes/__main__.py

@@ -59,38 +59,42 @@ def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
             filter="Finnigan RAW files (*.raw, *.RAW)")[0]
     if filename is not '' and os.path.isfile(filename)\
                           and not os.path.isdir(filename):
+        error = update_signal()
+        errormsg = []
         def runfnc():
             try:
-                d_set.clear()
-                chrom_s['timesarg'].clear()
+                [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]))
                     for i in load_raw(filename, settings.value("tmp_location"))]
             except rawprasslib.ParsingException as pex:
-                QtWidgets.QMessageBox.critical(
-                    parent, "Opening of the file has failed!",
+                errormsg.append("Opening of the file has failed!")
+                errormsg.append(
                     "File is incompatible with the rawprasslib, "
                     "canceling request!\n\n"
                     "Error message:\n{}".format(pex.args[0]))
+                error.signal.emit()
                 return
-            [i.clear() for i in (ms_s['params'],ms_s['headers'])]
             if autoparams == True:
                 try:
                     ms_s['params'], rawheaders = 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))]
+                    indicies = [sum(segments[:i+1]) for i in range(len(segments))]
                     ms_s['headers'] = np.split(rawheaders, indicies)[:-1]
                 except Exception as pex:
-                    QtWidgets.QMessageBox.critical(
-                        parent, "Parameters readout has failed!",
-                        "File is incompatible with the rawautoparams, "
-                        "no parameters loaded!\n\n"
-                        "Error message:\n{}".format(pex.args[0]))
+                    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()
+                    print("panoc baby")
             gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
             fn[0] = filename
             parent.setWindowTitle("Prasopes - {}".format(
                 os.path.basename(filename)))
             update.signal.emit()
+        error.signal.connect(lambda:
+            QtWidgets.QMessageBox.critical(parent, errormsg[0], errormsg[1]))
         loadthread.run = runfnc
         loadthread.start()
 
@@ -125,6 +129,28 @@ def update_spectrum(chromatogram, spect, ds, ms, fn, chrom, config):
         spect.get_figure().canvas.draw()
 
 
+def update_paramstable(table, ms, chrom):
+    if len(ms['params']) == 0:
+        table.setRowCount(0)
+        return
+    table.setRowCount(len(ms['params'][0]))
+    validator = QtGui.QDoubleValidator()
+    for row, paramname in enumerate(ms['params'][0]):
+        [table.setItem(row,col, QtWidgets.QTableWidgetItem())
+                for col in range(2)]
+        table.item(row,0).setText(paramname)
+        vals = [param[row] for param in ms['params'][1]]
+        if all([type(val) in [np.float32, np.float64] for val in vals]):
+            aver = np.average(vals)
+            minim = min(vals)
+            maxim = max(vals)
+            text = "{:.2f} (from {:.2f} to {:.2f})".format(aver, minim, maxim)
+        else:
+            values = [str(i) for i in np.unique(np.array(vals), axis=0)]
+            text = " or ".join(values)
+        table.item(row,1).setText(text)
+
+
 def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
             chrom, update, config, loadthread):
     dropurl = event.mimeData().urls()[0].toLocalFile()
@@ -353,6 +379,11 @@ def main():
     toolBar.addSeparator()
     toolBar.addAction(autozoomy)
 
+    paramsdock = QtWidgets.QDockWidget()
+    paramstable = dt.table(["name","value"], 100)
+    update.signal.connect(lambda: update_paramstable(paramstable, ms, chrom))
+    paramsdock.setWidget(paramstable)
+
     fileModel = QtWidgets.QFileSystemModel()
     fileModel.setRootPath('')
     activeDir = fileModel.index(config.value("open_folder"))
@@ -363,14 +394,12 @@ def main():
     dirview = QtWidgets.QListView()
     dirview.setModel(fileModel)
     treedock = QtWidgets.QDockWidget()
-
     def scrolltoonce():
         fileModel.directoryLoaded.disconnect(scrolltoonce)
         treeview.scrollTo(fileModel.index(config.value("open_folder")), 1)
     fileModel.directoryLoaded.connect(scrolltoonce)
     fileModel.directoryLoaded.connect(
             lambda: treeview.resizeColumnToContents(0))
-
     if not config.value("view/filebrowservisible",type=bool):
         treedock.hide()
     treedock.setWidget(QtWidgets.QWidget())
@@ -386,20 +415,19 @@ def main():
         update, config, loadthread, filename=fileModel.filePath(index))
     for i in [treeview.doubleClicked, dirview.doubleClicked, dirview.clicked]:
         i.connect(clickload)
-
     #fileModel gots stuck sometimes, better give it a separate thread
     #it complains at the start, but still works later 
     #and I did not found better solution
     treedockThread = QtCore.QThread()
     treedockThread.start()
     fileModel.moveToThread(treedockThread)
-
     def closeOverride(event, dock, action):
         action.setChecked(False)
         dock.hide()
         event.ignore()
     treedock.closeEvent = lambda event: closeOverride(
             event, treedock, filebrowseract)
+
     main_window.closeEvent = lambda event: treedockThread.quit()
     main_window.dragEnterEvent = lambda event: drag_entered(event)
     main_window.dropEvent = lambda event: dropped(
@@ -411,6 +439,7 @@ def main():
 
     main_window.addToolBar(QtCore.Qt.TopToolBarArea, toolBar)
     main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)
+    main_window.addDockWidget(QtCore.Qt.RightDockWidgetArea, paramsdock)
     main_window.setStatusBar(barHandler.statusBar)
 
     main_window.setFocus()

prasopes/datatools.py

 from PyQt5 import QtWidgets
+from PyQt5 import QtCore
 import numpy as np
 import os.path
 
@@ -37,3 +38,19 @@ def specttostr(spectrum, chrom_ds, fn, delim=" "):
 def clip_spectstr(spectrum, chrom_ds, fn):
     string = specttostr(spectrum, chrom_ds, fn, delim="\t")
     QtWidgets.QApplication.clipboard().setText(string)
+
+
+def table(labels, minsizex=600, minsizey=0):
+    """creates a reasonable table"""
+    table = QtWidgets.QTableWidget(columnCount=len(labels))
+    table.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
+                        QtWidgets.QSizePolicy.Expanding)
+    table.setHorizontalHeaderLabels(labels)
+    table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
+
+    for n in range(table.columnCount()):
+        table.horizontalHeader().setSectionResizeMode(
+            n, QtWidgets.QHeaderView.Stretch)
+    table.setMinimumSize(minsizex, minsizey)
+
+    return table

prasopes/drltools.py

@@ -367,22 +367,6 @@ def add_line(ds, drls, drlspectrum):
         ds, drls, drlspectrum))
 
 
-def iontable(labels):
-    """creates a table for ions"""
-    table = QtWidgets.QTableWidget(columnCount=len(labels))
-    table.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
-                        QtWidgets.QSizePolicy.Expanding)
-    table.setHorizontalHeaderLabels(labels)
-    table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
-
-    for n in range(table.columnCount()):
-        table.horizontalHeader().setSectionResizeMode(
-            n, QtWidgets.QHeaderView.Stretch)
-    table.setMinimumSize(600, 0)
-
-    return table
-
-
 def load_drltables(parent, dataset, drls, drlspectrum):
     filename = QtWidgets.QFileDialog.getOpenFileName(
             caption="Load DRL config tables",
@@ -680,8 +664,8 @@ def main_window(parent, ds, filename, cache, update_signal):
         for i in range(drls['cors'].value()):
             dcolums.append("corrected for ({})".format(i+1))
             dcolums.append("factor ({})".format(i+1))
-        drls['dt'] = iontable(dcolums)
-        drls['pt'] = iontable(["Name", "Mass (m/z)", "Peak width",
+        drls['dt'] = dt.table(dcolums)
+        drls['pt'] = dt.table(["Name", "Mass (m/z)", "Peak width",
                                "profile"])
         #TODO: DIRTY, DIRTY, DIRTY !!! do it nicer when I'll know how i want it
         [drls['dt'].horizontalHeader().setSectionResizeMode(

setup.py

@@ -26,7 +26,7 @@ setup(
                       'PyQt5;platform_system=="Darwin"',
                       'PyQt5-sip;platform_system=="Darwin"',
                       'matplotlib>=3.0.0',
-                      'rawprasslib'],
+                      'rawprasslib>=0.0.4'],
     entry_points={
         'console_scripts': [
             'prasopes = prasopes.__main__:main'