DRL evolution - pt5/5

* amount of "correct to" columns can be changed now in a software itself
* fix for deletion of multiple rows - now the SW survives
* time shift is now noted in the exported file (has been done in
previous commit, forget to note it)

prasopes/__main__.py

@@ -83,7 +83,8 @@ def main():
     drl_logger = logging.getLogger('drlLogger')
     logging.basicConfig()
     p_logger.setLevel("WARN")
-    drl_logger.setLevel("INFO")
+    #drl_logger.setLevel("INFO")
+    drl_logger.setLevel("DEBUG")
 
     graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
 

prasopes/drltools.py

@@ -6,6 +6,7 @@ from PyQt5 import QtWidgets
 from PyQt5 import QtGui
 from PyQt5 import QtPrintSupport
 from copy import copy
+import gc
 import matplotlib
 import numpy as np
 import prasopes.datatools as dt
@@ -19,12 +20,13 @@ matplotlib.use("Qt5Agg")
 logger = logging.getLogger('drlLogger')
 
 
-class HBar(QtWidgets.QFrame):
-    """horizontal bar class"""
+class StretchWidget(QtWidgets.QWidget):
+    """horizontal stretch class"""
     def __init__(self):
-        super(HBar, self).__init__()
+        super(StretchWidget, self).__init__()
         self._main = QtWidgets.QWidget()
-        self.setFrameShape(QtWidgets.QFrame.HLine)
+        self.setSizePolicy(QtWidgets.QSizePolicy.Expanding
+                          ,QtWidgets.QSizePolicy.Preferred)
 
 
 def floatize(table, row, column, nonneg=True):
@@ -79,7 +81,6 @@ def get_intensity(row, ds, drls):
 def get_daughterset(ds, drls):
     """Fuction to acquire the curves of the daugher ions"""
     logger.info("getting set of the daughter ions")
-    # TODO: write a less resources demanding function - probably "per-line"
     names = []
     times = ds['chrom_dat'][0, :] - drls['tshift'].value()
     intensities = []
@@ -87,7 +88,7 @@ def get_daughterset(ds, drls):
         if drls['dt'].cellWidget(row, 0).checkState() == 2:
             intensity = get_intensity(row, ds, drls)
             corlist = []
-            for i in range(drls['cors']):
+            for i in range(drls['cors'].value()):
                 cor = drls['dt'].cellWidget(row, 1+i*2).currentIndex() - 1
                 if cor not in (-2, -1):
                     factor = floatize(drls['dt'], row, 2+i*2, False)
@@ -108,7 +109,6 @@ def get_parentset(ds, drls):
     names = []
     times = ds['chrom_dat'][0, :]
     intensities = []
-    # TODO: resolve intensities trouble
     rowlist = []
     for row in range(drls['dt'].rowCount()):
         if drls['dt'].cellWidget(row, 0).checkState() == 2:
@@ -135,7 +135,6 @@ def update_drlspectrum(ds, drls, drlspectrum):
                        [200, 50, 0], [255, 0, 200], [0, 100, 0],
                        [0, 100, 255], [100, 100, 100]])
 
-    # TODO: write a less resources demanding function
     names, times, intensities = get_daughterset(ds, drls)
     for i in range(len(drlspectrum.lines)):
         drlspectrum.lines[0].remove()
@@ -190,7 +189,7 @@ def update_corrfors(drls):
     """update corrections selection layout of the daughter table"""
     ionlist = gettableitemlist(drls['pt'])
     for row in range(drls['dt'].rowCount()):
-        for i in range(drls['cors']):
+        for i in range(drls['cors'].value()):
             corfor = drls['dt'].cellWidget(row, 1+i*2)
             index = corfor.currentIndex()
             corfor.blockSignals(True)
@@ -226,13 +225,46 @@ def corr_changed(correction, ds, drls, drlspectrum):
         for j in range(drls['dt'].columnCount()):
             if correction == drls['dt'].cellWidget(i, 1+j*2):
                 row, column = i, 1 + j*2
+                logger.debug('''Change of the "correct to" on '''
+                             '''row {}, column {}'''.format(
+                                 row + 1, column + 1))
     if (drls['dt'].cellWidget(row, 0).checkState() == 2
        and floatize(drls['dt'], row, column+1, False) != 0):
         update_drlspectrum(ds, drls, drlspectrum)
 
 
+def corcount_changed(ds, drls, drlspectrum):
+    """routine called by change of the correction factors count"""
+    logger.info('''change in the correction count detected''')
+    diff = int(drls['cors'].value() - ((drls['dt'].columnCount() - 1) / 2))
+    if diff == 0:
+        return
+    elif diff > 0:
+        drls['dt'].setColumnCount(1 + (drls['cors'].value() * 2))
+        newcors = []
+        for col in range(drls['dt'].columnCount() - (diff * 2),
+                       drls['dt'].columnCount(), 2):
+            for row in range(drls['dt'].rowCount()):
+                    drls['dt'].setCellWidget(
+                        row, col, QtWidgets.QComboBox())
+                    drls['dt'].cellWidget(row, col).setFrame(False)
+                    drls['dt'].setItem(
+                        row, col+1, QtWidgets.QTableWidgetItem())
+                    newcors.append(drls['dt'].cellWidget(row, col))
+        list(map(lambda x: x.currentIndexChanged.connect(lambda:
+            corr_changed(x, ds, drls, drlspectrum)), newcors))
+        update_corrfors(drls)
+        dcolums = ["Name"]
+        for i in range(drls['cors'].value()):
+            dcolums.append("corrected for ({})".format(i+1))
+            dcolums.append("factor ({})".format(i+1))
+        drls['dt'].setHorizontalHeaderLabels(dcolums)
+    else:
+        drls['dt'].setColumnCount(1 + (drls['cors'].value() * 2))
+        update_drlspectrum(ds, drls, drlspectrum)
+
+
 def remove_rows(ds, drls, drlspectrum, rows=None):
-    # TODO: maybe nicer selection in future, but this works for now
     logger.info("remowing rows")
     if rows == None:
         rows = reversed(list(set(
@@ -243,7 +275,7 @@ def remove_rows(ds, drls, drlspectrum, rows=None):
         drls['dt'].removeRow(row)
         drls['pt'].removeRow(row)
         for i in range(drls['dt'].rowCount()):
-            for cornum in range(drls['cors']):
+            for cornum in range(drls['cors'].value()):
                 corfor = drls['dt'].cellWidget(i, 1+cornum*2)
                 cors.append(corfor)
                 corfor.disconnect()
@@ -258,8 +290,8 @@ def remove_rows(ds, drls, drlspectrum, rows=None):
                     corfor.setCurrentIndex(index-1)
                 else:
                     corfor.setCurrentIndex(index)
-    list(map(lambda x: x.currentIndexChanged.connect(lambda:
-        corr_changed(x, ds, drls, drlspectrum)), cors))
+        list(map(lambda x: x.currentIndexChanged.connect(lambda:
+            corr_changed(x, ds, drls, drlspectrum)), cors))
 
 
 def add_line(ds, drls, drlspectrum):
@@ -294,7 +326,7 @@ def add_line(ds, drls, drlspectrum):
     drls['dt'].setItem(newrow, 0, dname)
     drls['dt'].setCellWidget(newrow, 0, checkbox)
 
-    for i in range(drls['cors']):
+    for i in range(drls['cors'].value()):
         col = copy(1+i*2)
         drls['dt'].setCellWidget(newrow, col, QtWidgets.QComboBox())
         drls['dt'].cellWidget(newrow, col).setFrame(False)
@@ -303,11 +335,8 @@ def add_line(ds, drls, drlspectrum):
     drls['pt'].blockSignals(False)
     drls['dt'].blockSignals(False)
 
-    #dirty hack, but if if cycle is applied it assigns all cellWidgets
-    #to a maximal value of i (as this is the value of i after the end
-    #of the cycle)
     cors = list(map(lambda x: drls['dt'].cellWidget(newrow, 1+x*2),
-                    range(drls['cors'])))
+                    range(drls['cors'].value())))
     list(map(lambda x: x.currentIndexChanged.connect(lambda:
         corr_changed(x, ds, drls, drlspectrum)), cors))
 
@@ -354,7 +383,6 @@ def load_drltables(parent, dataset, drls, drlspectrum):
             corrections.append([])
         for i in range(1, len(rawdata)):
             rawline = rawdata[i].split(",")
-            # TODO: rawline[4] can be -1 - decide if accept this behaviour
             n = len(rawline)
             if n < 6 or not n % 2 == 0 or (int(rawline[3]) not in
                 range(3)) or not (set(map(int, rawline[4:n:2])) &
@@ -377,6 +405,7 @@ def load_drltables(parent, dataset, drls, drlspectrum):
             drls['pt'].item(i, 1).setText(start_masses[i])
             drls['pt'].item(i, 2).setText(end_masses[i])
         # and after that the daughter table
+        drls['cors'].setValue(int(1 + (len(names) / 2)))
         for i in range(len(names)):
             for j in range(int((len(rawline)-4)/2)):
                 drls['dt'].cellWidget(i, 1+j*2).setCurrentIndex(
@@ -393,7 +422,7 @@ def save_drlconfig(drls, parent, exp_f_name=None):
             "csv", parent)
     if exp_f_name is not '':
         corlist = []
-        for i in range(drls['cors']):
+        for i in range(drls['cors'].value()):
             corlist.append("corrected_to_{}, factor_{} ".format(
                 i+1, i+1))
         cortext = ", ".join(corlist)
@@ -405,7 +434,7 @@ def save_drlconfig(drls, parent, exp_f_name=None):
             for i in range(3):
                 vals.append(drls['pt'].item(row, i).text())
             vals.append(drls['dt'].cellWidget(row, 0).checkState())
-            for i in range(drls['cors']):
+            for i in range(drls['cors'].value()):
                 vals.append(drls['dt'].cellWidget(row, 1+i*2).currentIndex())
                 vals.append(drls['dt'].item(row, 2+i*2).text())
             expf.write("{}\n".format((",".join(map(str, vals)))))
@@ -553,6 +582,7 @@ def key_pressed(event, ds, drls, drlspectrum):
         and event.modifiers().__int__() == QtCore.Qt.ControlModifier:
         paste_clip(ds, drls, drlspectrum)
 
+
 def select_all_btn_up(ds, drls, drlspectrum, state=None):
     logger.info('''Change of the select-all button detected''')
     if state in (0,2):
@@ -585,11 +615,11 @@ def main_window(parent, ds, filename, cache):
 
     # pt = parenttable
     # dt = daughtertable
-    drls = dict(pt=None, dt=None, tshift=None, cors=3, rel=None,
+    drls = dict(pt=None, dt=None, tshift=None, cors=None, rel=None,
                 checkAll=None)
 
     window = QtWidgets.QMainWindow(
-        parent, windowTitle='Delayed reactant labelling')
+        parent, windowTitle='Delayed reactant labeling')
     main_widget = QtWidgets.QWidget(window)
     window.setCentralWidget(main_widget)
 
@@ -611,10 +641,9 @@ def main_window(parent, ds, filename, cache):
     time_title = QtWidgets.QLabel("Time shift (min):")
     drls['tshift'] = QtWidgets.QDoubleSpinBox(
             minimum=-100, maximum=1440, decimals=3)
-
     drls['rel'] = QtWidgets.QCheckBox("Steady state approximation")
-
     drls['checkAll'] = QtWidgets.QCheckBox("Select all")
+    drls['cors'] = QtWidgets.QSpinBox(minimum=0)
 
     drl_load = QtWidgets.QPushButton("&Load")
     drl_save = QtWidgets.QPushButton("&Save")
@@ -628,7 +657,8 @@ def main_window(parent, ds, filename, cache):
 
     if cache == [None, None]:
         dcolums = ["Name"]
-        for i in range(drls['cors']):
+        drls['cors'].setValue(3)
+        for i in range(drls['cors'].value()):
             dcolums.append("corrected for ({})".format(i+1))
             dcolums.append("factor ({})".format(i+1))
         drls['dt'] = iontable(dcolums)
@@ -661,16 +691,14 @@ def main_window(parent, ds, filename, cache):
 
     drls['pt'].itemChanged.connect(lambda item: ptable_changed(
         item.row(), item.column(), ds, drls, chromplot))
-
     drls['dt'].itemChanged.connect(lambda item: dtable_changed(
         item.row(), item.column(), ds, drls, chromplot))
-
     drls['tshift'].valueChanged.connect(lambda: update_drlspectrum(
         ds, drls, chromplot))
-
+    drls['cors'].valueChanged.connect(lambda: corcount_changed(
+        ds, drls, chromplot))
     drls['rel'].stateChanged.connect(lambda: update_drlspectrum(
         ds, drls, chromplot))
-
     drls['checkAll'].stateChanged.connect(lambda state:
         select_all_btn_up(ds, drls, chromplot, state))
 
@@ -683,10 +711,7 @@ def main_window(parent, ds, filename, cache):
     actionBar.addWidget(drl_load)
     actionBar.addWidget(drl_save)
     actionBar.addWidget(drl_print)
-    stretchWidget = QtWidgets.QWidget()
-    stretchWidget.setSizePolicy(QtWidgets.QSizePolicy.Expanding
-                               ,QtWidgets.QSizePolicy.Preferred)
-    actionBar.addWidget(stretchWidget)
+    actionBar.addWidget(StretchWidget())
     actionBar.addWidget(drl_export)
     actionBar.addWidget(close)
 
@@ -694,8 +719,15 @@ def main_window(parent, ds, filename, cache):
     dtdock.setWidget(QtWidgets.QWidget())
     dtdock_layout = QtWidgets.QVBoxLayout(dtdock.widget())
     dtdock.setWindowTitle("Corrected ions table")
-    dtdock_layout.addWidget(drls['checkAll'])
+    dt_butlayout = QtWidgets.QHBoxLayout()
+    dt_butlayout.addWidget(drls['checkAll'])
+    dt_butlayout.addWidget(StretchWidget())
+    dt_butlayout.addWidget(QtWidgets.QLabel("Number of corrections:"))
+    dt_butlayout.addWidget(drls['cors'])
+    dt_butlayout.addWidget(StretchWidget())
+    dtdock_layout.addLayout(dt_butlayout)
     dtdock_layout.addWidget(drls['dt'])
+    window.addDockWidget(QtCore.Qt.BottomDockWidgetArea, dtdock)
 
     ptdock = QtWidgets.QDockWidget()
     ptdock.setWidget(QtWidgets.QWidget())
@@ -707,8 +739,6 @@ def main_window(parent, ds, filename, cache):
     pt_butlayout.addWidget(btn_rem)
     pt_butlayout.addStretch(0)
     ptdock_layout.addLayout(pt_butlayout)
-
-    window.addDockWidget(QtCore.Qt.BottomDockWidgetArea, dtdock)
     window.addDockWidget(QtCore.Qt.RightDockWidgetArea, ptdock)
 
     main_layout = QtWidgets.QVBoxLayout(main_widget)