Created project tree

prasopes/__main__.py

+#!/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
+from rawParse import load_raw
+import graph_tools as gt
+import file_tools as ft
+import os.path
+import sys
+import matplotlib
+import numpy as np
+import logging
+matplotlib.use("Qt5Agg")
+
+
+
+
+if __name__ == "__main__":
+    # ds for data_set, ms for mass_spec_dataset, chrom for chrom_dataset
+    ds = dict(chrom_dat=None, masses=None, matrix=None)
+    ms = dict(x=[0], y=[0], line=None, annotation=[],
+              name="Spectrum", xlabel="m/z", ylabel="ion count")
+    chrom = dict(x=[0], y=[0], line=None, t_start=None, t_end=None,
+                 name="Chromatogram", xlabel="time(min)",
+                 ylabel="total ion count")
+    filename = [None]
+
+    p_logger = logging.getLogger('parseLogger')
+    logging.basicConfig()
+    p_logger.setLevel("WARN")
+
+    graph = Figure(figsize=(5, 4), dpi=100)
+    graph.patch.set_facecolor("None")
+
+    chromatogram = graph.add_subplot(211, facecolor=(1, 1, 1, 0.8))
+    spectrum = graph.add_subplot(212, facecolor=(1, 1, 1, 0.8))
+    graph.tight_layout()
+
+    mpl_canvas = FigureCanvas(graph)
+    mpl_canvas.setStyleSheet("background-color:transparent;")
+    mpl_canvas.setAutoFillBackground(False)
+    mpl_canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
+    
+    gt.pan_factory(chromatogram)
+    gt.zoom_factory(chromatogram, 1.15)
+    gt.pan_factory(spectrum, ms)
+    gt.zoom_factory(spectrum, 1.15, ms)
+    gt.mass_selector = SpanSelector(
+        spectrum, lambda x_min, x_max: gt.pick_masses(
+            x_min, x_max, spectrum, ms),
+        'horizontal', useblit=True, rectprops=dict(
+            alpha=0.15, facecolor='purple'), button=3)
+    gt.time_selector = SpanSelector(
+         chromatogram, lambda x_min, x_max: gt.pick_times(
+             x_min, x_max, spectrum, ds, chromatogram, ms, chrom), 
+         'horizontal', useblit=True, rectprops=dict(
+             alpha=0.15, facecolor='purple'), button=3)
+
+    app = QtWidgets.QApplication(sys.argv)
+    main_window = QtWidgets.QMainWindow()
+    main_window.setWindowTitle("Prasopes")
+
+    file_menu = QtWidgets.QMenu('&File', main_window)
+    main_window.menuBar().addMenu(file_menu)
+    file_menu.addAction('&Open..', lambda: ft.open_file(
+        chromatogram, spectrum, ds, ms, filename, chrom),
+        QtCore.Qt.CTRL + QtCore.Qt.Key_O)
+    file_menu.addAction('&Export..', lambda: ft.export(
+        ms, chrom, filename), QtCore.Qt.CTRL + QtCore.Qt.Key_E)
+    file_menu.addAction('&Quit', main_window.close,
+                        QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
+
+    main_widget = QtWidgets.QWidget(main_window)
+    main_window.setCentralWidget(main_widget)
+
+    layout = QtWidgets.QVBoxLayout(main_widget)
+    layout.addWidget(mpl_canvas)
+    mpl_canvas.setFocus()
+
+    if len(sys.argv) == 2:
+        raw_file = sys.argv[1]
+        filename[0] = raw_file
+        ds['chrom_dat'], ds['masses'], ds['matrix'] = load_raw(raw_file)
+        gt.populate(chromatogram, spectrum, ds, ms, chrom)
+    else:
+        gt.pop_plot(spectrum, ms)
+        gt.pop_plot(chromatogram, chrom)
+
+    main_window.show()
+    sys.exit(app.exec_())

prasopes/file_tools.py

+from PyQt5 import QtCore
+from PyQt5 import QtWidgets
+from rawParse import load_raw
+import os.path
+import logging
+import graph_tools as gt
+
+def open_file(chrom_plot, spc, d_set, ms_s, fn, chrom_s):
+    """Returns chromatogram, masses and ion intensities"""
+    fn[0] = QtWidgets.QFileDialog.getOpenFileName(
+            caption="Open spectrum",
+            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
+    if fn[0] is not'':
+        d_set['chrom_dat'], d_set['masses'], d_set['matrix'] \
+             = load_raw(fn[0])
+        gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
+
+
+def export(mass_spec, chrom_spec, fn):
+    """exports the chromatogram into the .dat file format"""
+    if fn[0] is None:
+        QtWidgets.QMessageBox.warning(
+            main_window, "Export spectrum",
+            "Nothing to export, cancelling request")
+        return
+    exp_f_name = QtWidgets.QFileDialog.getSaveFileName(
+            caption="Export spectrum",
+            filter="dat table format (*.dat)")[0]
+    if exp_f_name is not '':
+        # fix for Qt5 "Feature"
+        if exp_f_name[-4:] != '.dat':
+            exp_f_name = exp_f_name + ".dat"
+            if os.path.isfile(exp_f_name):
+                quest = QtWidgets.QMessageBox.warning(
+                    main_window, "Export spectrum",
+                    "{} already exists.\n Do you want to replace it?"
+                    .format(os.path.basename(exp_f_name)),
+                    QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
+                if(hex(quest)) == "0x10000":
+                    return
+        expf = open(exp_f_name, 'w')
+        expf.write("mass ion_count\n" 
+                   "m/z\n" 
+                   "{}_{:.4}-{:.4}_minutes_of_the_aquisition\n".format(
+                       os.path.basename(fn[0]),
+                       chrom_spec['t_start'], chrom_spec['t_end']))
+        for i in range(len(mass_spec['x'])): 
+            expf.write("{} {}\n".format(
+                mass_spec['x'][i], mass_spec['y'][i]))
+        expf.close()

prasopes.py → prasopes/graph_tools.py

-#!/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
-from rawParse import load_raw
-import os.path
-import sys
 import matplotlib
 import numpy as np
 import logging
-matplotlib.use("Qt5Agg")
-
+import file_tools as ft
 
 def zoom_factory(axis, base_scale, plot_data=dict()):
     """returns zooming functionality to axis"""
@@ -141,27 +131,6 @@ def pick_times(x_min, x_max, mpl_spectrum, data_set, mpl_chromatogram,
     dots_y = data_set['chrom_dat'][1, start_scan:end_scan]
     mpl_chromatogram.plot(dots_x, dots_y, 'b.')
 
-
-def populate(mpl_chromatogram, mpl_spectrum, data_set,
-             mass_spect, chrom_spect):
-    """populate the GUI plots with desired dataset"""
-    mass_spect['annotation'].clear()
-    mpl_spectrum.clear()
-    mpl_chromatogram.clear()
-
-    mass_spect['x'] = data_set['masses']
-    mass_spect['y'] = np.mean(data_set['matrix'], axis=0)
-    pop_plot(mpl_spectrum, mass_spect)
-    mpl_spectrum.figure.canvas.draw()
-
-    chrom_spect['x'] = data_set['chrom_dat'][0, :]
-    chrom_spect['y'] = data_set['chrom_dat'][1, :]
-    chrom_spect['t_start'] = data_set['chrom_dat'][0, 0]
-    chrom_spect['t_end'] = data_set['chrom_dat'][0, -1]
-    pop_plot(mpl_chromatogram, chrom_spect)
-    mpl_chromatogram.figure.canvas.draw()
-
-
 def ann_spec(ms_spec, msdata, ann_limit=0.01):
     """annotate spectrum
     
@@ -220,7 +189,6 @@ def ann_spec(ms_spec, msdata, ann_limit=0.01):
             '{0:.2f}'.format(msdata['x'][i]), xy=(msdata['x'][i], msdata['y'][i]),
             textcoords='data'))
 
-
 def pop_plot(plot, plot_data):
     """Define and populate plot"""
     plot_data['line'] = plot.plot(plot_data['x'], plot_data['y'])
@@ -233,121 +201,21 @@ def pop_plot(plot, plot_data):
     if "annotation" in plot_data:
         ann_spec(plot, plot_data)
 
+def populate(mpl_chromatogram, mpl_spectrum, data_set,
+             mass_spect, chrom_spect):
+    """populate the GUI plots with desired dataset"""
+    mass_spect['annotation'].clear()
+    mpl_spectrum.clear()
+    mpl_chromatogram.clear()
 
-def open_file(chrom_plot, spc, d_set, ms_s, fn, chrom_s):
-    """Returns chromatogram, masses and ion intensities"""
-    fn[0] = QtWidgets.QFileDialog.getOpenFileName(
-            caption="Open spectrum",
-            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
-    if fn[0] is not'':
-        d_set['chrom_dat'], d_set['masses'], d_set['matrix'] \
-             = load_raw(fn[0])
-        populate(chrom_plot, spc, d_set, ms_s, chrom_s)
-
-
-def export(mass_spec, chrom_spec, fn):
-    """exports the chromatogram into the .dat file format"""
-    if fn[0] is None:
-        QtWidgets.QMessageBox.warning(
-            main_window, "Export spectrum",
-            "Nothing to export, cancelling request")
-        return
-    exp_f_name = QtWidgets.QFileDialog.getSaveFileName(
-            caption="Export spectrum",
-            filter="dat table format (*.dat)")[0]
-    if exp_f_name is not '':
-        # fix for Qt5 "Feature"
-        if exp_f_name[-4:] != '.dat':
-            exp_f_name = exp_f_name + ".dat"
-            if os.path.isfile(exp_f_name):
-                quest = QtWidgets.QMessageBox.warning(
-                    main_window, "Export spectrum",
-                    "{} already exists.\n Do you want to replace it?"
-                    .format(os.path.basename(exp_f_name)),
-                    QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
-                if(hex(quest)) == "0x10000":
-                    return
-        expf = open(exp_f_name, 'w')
-        expf.write("mass ion_count\n" 
-                   "m/z\n" 
-                   "{}_{:.4}-{:.4}_minutes_of_the_aquisition\n".format(
-                       os.path.basename(fn[0]),
-                       chrom_spec['t_start'], chrom_spec['t_end']))
-        for i in range(len(mass_spec['x'])): 
-            expf.write("{} {}\n".format(
-                mass_spec['x'][i], mass_spec['y'][i]))
-        expf.close()
-
-
-if __name__ == "__main__":
-    # ds for data_set, ms for mass_spec_dataset, chrom for chrom_dataset
-    ds = dict(chrom_dat=None, masses=None, matrix=None)
-    ms = dict(x=[0], y=[0], line=None, annotation=[],
-              name="Spectrum", xlabel="m/z", ylabel="ion count")
-    chrom = dict(x=[0], y=[0], line=None, t_start=None, t_end=None,
-                 name="Chromatogram", xlabel="time(min)",
-                 ylabel="total ion count")
-    filename = [None]
-
-    p_logger = logging.getLogger('parseLogger')
-    logging.basicConfig()
-    p_logger.setLevel("WARN")
-
-    graph = Figure(figsize=(5, 4), dpi=100)
-    graph.patch.set_facecolor("None")
-
-    chromatogram = graph.add_subplot(211, facecolor=(1, 1, 1, 0.8))
-    spectrum = graph.add_subplot(212, facecolor=(1, 1, 1, 0.8))
-    graph.tight_layout()
-
-    mpl_canvas = FigureCanvas(graph)
-    mpl_canvas.setStyleSheet("background-color:transparent;")
-    mpl_canvas.setAutoFillBackground(False)
-    mpl_canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
-    
-    pan_factory(chromatogram)
-    zoom_factory(chromatogram, 1.15)
-    pan_factory(spectrum, ms)
-    zoom_factory(spectrum, 1.15, ms)
-    mass_selector = SpanSelector(
-        spectrum, lambda x_min, x_max: pick_masses(
-            x_min, x_max, spectrum, ms),
-        'horizontal', useblit=True, rectprops=dict(
-            alpha=0.15, facecolor='purple'), button=3)
-    time_selector = SpanSelector(
-         chromatogram, lambda x_min, x_max: pick_times(
-             x_min, x_max, spectrum, ds, chromatogram, ms, chrom), 
-         'horizontal', useblit=True, rectprops=dict(
-             alpha=0.15, facecolor='purple'), button=3)
-
-    app = QtWidgets.QApplication(sys.argv)
-    main_window = QtWidgets.QMainWindow()
-
-    file_menu = QtWidgets.QMenu('&File', main_window)
-    main_window.menuBar().addMenu(file_menu)
-    file_menu.addAction('&Open..', lambda: open_file(
-        chromatogram, spectrum, ds, ms, filename, chrom),
-        QtCore.Qt.CTRL + QtCore.Qt.Key_O)
-    file_menu.addAction('&Export..', lambda: export(
-        ms, chrom, filename), QtCore.Qt.CTRL + QtCore.Qt.Key_E)
-    file_menu.addAction('&Quit', main_window.close,
-                        QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
-
-    main_widget = QtWidgets.QWidget(main_window)
-    main_window.setCentralWidget(main_widget)
-
-    layout = QtWidgets.QVBoxLayout(main_widget)
-    layout.addWidget(mpl_canvas)
-    mpl_canvas.setFocus()
-
-    if len(sys.argv) == 2:
-        raw_file = sys.argv[1]
-        filename[0] = raw_file
-        ds['chrom_dat'], ds['masses'], ds['matrix'] = load_raw(raw_file)
-        populate(chromatogram, spectrum, ds, ms, chrom)
-    else:
-        pop_plot(spectrum, ms)
-        pop_plot(chromatogram, chrom)
+    mass_spect['x'] = data_set['masses']
+    mass_spect['y'] = np.mean(data_set['matrix'], axis=0)
+    pop_plot(mpl_spectrum, mass_spect)
+    mpl_spectrum.figure.canvas.draw()
 
-    main_window.show()
-    sys.exit(app.exec_())
+    chrom_spect['x'] = data_set['chrom_dat'][0, :]
+    chrom_spect['y'] = data_set['chrom_dat'][1, :]
+    chrom_spect['t_start'] = data_set['chrom_dat'][0, 0]
+    chrom_spect['t_end'] = data_set['chrom_dat'][0, -1]
+    pop_plot(mpl_chromatogram, chrom_spect)
+    mpl_chromatogram.figure.canvas.draw()

setup.py

+from setuptools import setup
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setup(
+    name="prasopes",
+    version="0.0.1",
+    author="Jan Zelenka",
+    author_email="3yanyanyan@gmail.com",
+    description="Thermo/Finnigan .raw file viewer based on rawprasslib",
+    long_description=long_description,
+    url="https://gitlab.science.ru.nl/jzelenka/prasopes",
+    packages=['prasopes'],
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+        "Development Status :: 3-Alpha",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Chemistry",
+        ],
+    install_requires=['numpy', 'PyQt5-sip', 'matplotlib', 'rawprasslib']
+    )