def test_getAddedChannel(self):
TOF = pySPM.ITA(data)
img1 = TOF.getAddedImageByMass(107)
img2, CH = TOF.getAddedImageByName('Ag', strict=True)
assert len(CH) == 1
assert CH[0]['assign'] == 'Ag+'
assert np.all(img1.pixels == img2.pixels)
def open(self, t_filename=None):
settings = QSettings(QSettings.IniFormat, QSettings.UserScope, "pySPM",
"pySPM")
if t_filename is None:
home = QDir.cleanPath(os.getenv("HOMEPATH"))
path = settings.value("lastPath", home)
self.filename = QFileDialog.getOpenFileName(
None, "Choose measurement file", path, "*.ita")
else:
self.filename = t_filename
check_file = QFileInfo(self.filename)
self.setWindowTitle(check_file.fileName())
if not check_file.exists() or not check_file.isFile():
return
settings.setValue("lastPath", check_file.path())
self.ita = pySPM.ITA(self.filename)
self.t, self.S = self.ita.getSpectrum(time=True)
self.sf, self.k0 = self.ita.get_mass_cal()
self.mass = pySPM.utils.time2mass(self.t, self.sf, self.k0)
self.spec = self.ax.plot(self.mass, self.S)[0]
SatLevel = self.ita.size['pixels']['x'] * self.ita.size['pixels'][
'y'] * self.ita.Nscan
self.sat_level = self.ax.axhline(SatLevel, color='r')
if 'pySPM' in self.ita.root.goto("MassScale"):
self.MassCal = []
N = self.ita.root.goto("MassScale/pySPM/N").get_ulong()
for i in range(N):
elt = self.ita.root.goto("MassScale/pySPM/" + str(i) +
"/elt").value.decode('utf8')
mass = self.ita.root.goto("MassScale/pySPM/" + str(i) +
"/mass").get_double()
time = self.ita.root.goto("MassScale/pySPM/" + str(i) +
"/time").get_double()
self.MassCal.append(dict(elt=elt, mass=mass, time=time))
else:
self.MassCal = []
for x in self.ita.root.goto("MassScale/calib"):
if x.name == 'assign':
self.MassCal.append({'elt': x.get_string()})
if x.name == 'mcp':
mcp = struct.unpack("<10d", x.value)
self.MassCal[-1]['time'] = mcp[0]
self.MassCal[-1]['mass'] = mcp[1]
self.DoMassCal()
def __init__(self, filename=None):
super(QWidget, self).__init__()
self.ui = Ui_slicer()
self.ui.setupUi(self)
self.canvas = self.ui.mpl.canvas
self.fig = self.ui.mpl.canvas.fig
self.initPlotLayout()
self.level = None
if filename is None:
if len(sys.argv) < 2:
self.path, _ = QFileDialog.getOpenFileName(
self, "ITA Image", "", "(*.ITA)")
else:
# If an argument is sent to the script, the first argument will be used as a Path. Very usefull for debugging the script without having to selectr the folder each time with window dialog
self.path = sys.argv[1]
else:
self.path = filename
if not os.path.exists(self.path):
raise Exception("File \"{}\" is not found".format(self.path))
if os.path.exists(self.path + ".level.npy"):
self.level = np.load(self.path + ".level.npy")
self.curs = [0, 0, 0]
self.volume = None
self.ITA = pySPM.ITA(self.path)
for i, x in enumerate(self.ITA.get_masses()):
self.ui.peakList.setRowCount(i + 1)
self.ui.peakList.setItem(i, 0, QTableWidgetItem(x['assign']))
self.ui.peakList.setItem(
i, 1, QTableWidgetItem("{:.2f}u".format((x['cmass']))))
self.ui.peakList.setItem(
i, 2,
QTableWidgetItem("{:.2f}u".format(x['umass'] - x['lmass'])))
self.ui.peakList.show()
self.ui.cmap.currentIndexChanged.connect(self.plot)
self.ui.prof1daxis.currentIndexChanged.connect(self.plot)
self.ui.peakList.cellClicked.connect(self.load_channel)
self.canvas.mpl_connect('button_press_event', self.on_pick)
self.flatAction = QAction("Flatten substrate from this channel")
self.flatAction.triggered.connect(self.flatten)
self.ui.correction.stateChanged.connect(self.plot)
self.ui.peakList.addAction(self.flatAction)
self.ui.status.setText("IDLE")
def test_SI_image(self):
TOF = pySPM.ITA(data)
assert TOF.img.pixels.shape[0] == TOF.size['pixels']['y']
assert TOF.img.pixels.shape[1] == TOF.size['pixels']['x']
def test_ITA_loading(self):
TOF = pySPM.ITA(data)