class AnnotatePeaks(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotatePeaks, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Peaks')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Peaks')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_peaks = QListWidgetAddRemove()
self.lw_peaks.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_peaks)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_start = QDoubleSpinBox()
self.add_start.setRange(-1, 12)
self.add_start.setDecimals(3)
self.add_start.setSuffix('ppm')
self.add_start.setSingleStep(0.001)
self.add_end = QDoubleSpinBox()
self.add_end.setRange(-1, 12)
self.add_end.setDecimals(3)
self.add_end.setSuffix('ppm')
self.add_end.setSingleStep(0.001)
addc = QPushButton('Add')
addc.clicked.connect(self.onPeakAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onPeakAdd)
loadc = QPushButton("Import from file")
loadc.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'folder-open-document.png')))
loadc.clicked.connect(self.onPeakImport)
metabh = QPushButton("Auto match via MetaboHunter")
metabh.setIcon(
QIcon(os.path.join(utils.scriptdir, 'icons', 'metabohunter.png')))
metabh.clicked.connect(self.onPeakImportMetabohunter)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_start)
vboxh.addWidget(self.add_end)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vbox.addWidget(loadc)
vbox.addWidget(metabh)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/peaks', self.lw_peaks,
(self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onPeakAdd(self):
c = self.config.get(
'annotation/peaks'
)[:] # Create new list to force refresh on reassign
c.append((self.add_label.text(), float(self.add_start.value()),
float(self.add_end.value())))
self.config.set('annotation/peaks', c)
def onPeakRemove(self):
i = self.lw_peaks.removeItemAt(self.lw_peaks.currentRow())
# c = self.map_list_fwd(i.text())
def onPeakImport(self):
filename, _ = QFileDialog.getOpenFileName(
self.parent(), 'Load peak annotations from file', '',
"All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)"
)
if filename:
c = self.config.get(
'annotation/peaks'
)[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append(row[0], float(row[1]), float(row[2]))
self.config.set('annotation/peaks', c)
def onPeakImportMetabohunter(self):
c = self.config.get(
'annotation/peaks'
)[:] # Create new list to force refresh on reassign
t = self.parent().current_tool
dlg = MetaboHunter(self)
if dlg.exec_():
if 'spc' in t.data:
# We have a spectra; calcuate mean; reduce size if required
spc = t.data['spc']
n = spc.data.shape[1]
ppm = spc.ppm
spcd = np.mean(spc.data, axis=0)
# Set a hard limit on the size of data we submit to be nice.
if n > 3000:
# Calculate the division required to be under the limit
d = np.ceil(float(n) / 3000)
# Trim axis to multiple of divisor
trim = (n // d) * d
spcd = spcd[:trim]
ppm = ppm[:trim]
# Mean d shape
spcd = np.mean(spcd.reshape(-1, d), axis=1)
ppm = np.mean(ppm.reshape(-1, d), axis=1)
# Submit with settings
hmdbs = metabohunter.request(
ppm,
spcd,
metabotype=dlg.config.get('Metabotype'),
database=dlg.config.get('Database Source'),
ph=dlg.config.get('Sample pH'),
solvent=dlg.config.get('Solvent'),
frequency=dlg.config.get('Frequency'),
method=dlg.config.get('Method'),
noise=dlg.config.get('Noise Threshold'),
confidence=dlg.config.get('Confidence Threshold'),
tolerance=dlg.config.get('Tolerance'))
ha = np.array(hmdbs)
unique_hmdbs = set(hmdbs)
if None in unique_hmdbs:
unique_hmdbs.remove(None)
# Extract out regions
for hmdb in unique_hmdbs:
hb = np.diff(ha == hmdb)
# These are needed to ensure markers are there for objects starting and ending on array edge
if ha[0] == hmdb:
hb[0] == True
if ha[-1] == hmdb:
hb[-1] == True
idx = np.nonzero(hb)[0]
idx = idx.reshape(-1, 2)
if dlg.config.get(
'convert_hmdb_ids_to_names'
) and hmdb in METABOHUNTER_HMDB_NAME_MAP.keys():
label = METABOHUNTER_HMDB_NAME_MAP[hmdb]
else:
label = hmdb
# Now we have an array of all start, stop positions for this item
for start, stop in idx:
c.append((label, ppm[start], ppm[stop]))
self.config.set('annotation/peaks', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%.2f\t%.2f" % tuple(x)
self.fwd_map_cache[s] = x
return s
class QGraphicsSceneExtend(QGraphicsScene):
def __init__(self, parent, *args, **kwargs):
super(QGraphicsSceneExtend, self).__init__(parent, *args, **kwargs)
self.m = parent.m
self.config = ConfigManager()
# These config settings are transient (ie. not stored between sessions)
self.config.set_defaults({
'mode': EDITOR_MODE_NORMAL,
'font-family': 'Arial',
'font-size': '12',
'text-bold': False,
'text-italic': False,
'text-underline': False,
'text-color': '#000000',
'color-border': None, # '#000000',
'color-background': None,
})
# Pre-set these values (will be used by default)
self.config.set('color-background', '#5555ff')
self.background_image = QImage(os.path.join(utils.scriptdir, 'icons', 'grid100.png'))
if settings.get('Editor/Show_grid'):
self.showGrid()
else:
self.hideGrid()
self.mode = EDITOR_MODE_NORMAL
self.mode_current_object = None
self.annotations = []
def mousePressEvent(self, e):
if self.config.get('mode') != EDITOR_MODE_NORMAL:
for i in self.selectedItems():
i.setSelected(False)
if self.config.get('mode') == EDITOR_MODE_TEXT:
tw = AnnotationTextItem(position=e.scenePos())
elif self.config.get('mode') == EDITOR_MODE_REGION:
tw = AnnotationRegionItem(position=e.scenePos())
elif self.config.get('mode') == EDITOR_MODE_ARROW:
tw = AnnotationRegionItem(position=e.scenePos())
self.addItem(tw)
self.mode_current_object = tw
tw._createFromMousePressEvent(e)
tw.importStyleConfig(self.config)
self.annotations.append(tw)
else:
for i in self.selectedItems():
i.setSelected(False)
super(QGraphicsSceneExtend, self).mousePressEvent(e)
def mouseMoveEvent(self, e):
if self.config.get('mode') == EDITOR_MODE_TEXT and self.mode_current_object:
self.mode_current_object._resizeFromMouseMoveEvent(e)
elif self.config.get('mode') == EDITOR_MODE_REGION and self.mode_current_object:
self.mode_current_object._resizeFromMouseMoveEvent(e)
else:
super(QGraphicsSceneExtend, self).mouseMoveEvent(e)
def mouseReleaseEvent(self, e):
if self.config.get('mode'):
self.mode_current_object.setSelected(True)
self.mode_current_object.setFocus()
self.config.set('mode', EDITOR_MODE_NORMAL)
self.mode_current_object = None
super(QGraphicsSceneExtend, self).mouseReleaseEvent(e)
def showGrid(self):
self.setBackgroundBrush(QBrush(self.background_image))
def hideGrid(self):
self.setBackgroundBrush(QBrush(None))
def onSaveAsImage(self):
filename, _ = QFileDialog.getSaveFileName(self.m, 'Save current figure', '', "Tagged Image File Format (*.tif);;\
Portable Network Graphics (*.png)")
if filename:
self.saveAsImage(filename)
def saveAsImage(self, f):
self.image = QImage(self.sceneRect().size().toSize(), QImage.Format_ARGB32)
self.image.fill(Qt.white)
painter = QPainter(self.image)
self.render(painter)
self.image.save(f)
def addApp(self, app, position=None):
i = ToolItem(self, app, position=position)
self.addItem(i)
#i.onShow()
return i
def removeApp(self, app):
i = app.editorItem
i.hide()
self.removeItem(i)
app.editorItem = None
def dragEnterEvent(self, e):
if e.mimeData().hasFormat('application/x-pathomx-app') or e.mimeData().hasFormat('text/uri-list'):
e.accept()
else:
e.ignore()
def dragMoveEvent(self, e):
e.accept()
def dropEvent(self, e):
scenePos = e.scenePos() - QPointF(32, 32)
if e.mimeData().hasFormat('application/x-pathomx-app'):
try:
app_id = str(e.mimeData().data('application/x-pathomx-app'), 'utf-8') # Python 3
except:
app_id = str(e.mimeData().data('application/x-pathomx-app')) # Python 2
e.setDropAction(Qt.CopyAction)
a = app_launchers[app_id](self.m, position=scenePos, auto_focus=False)
#self.centerOn(a.editorItem)
e.accept()
elif e.mimeData().hasFormat('text/uri-list'):
for ufn in e.mimeData().urls():
fn = ufn.path()
fnn, ext = os.path.splitext(fn)
ext = ext.strip('.')
if ext in file_handlers:
a = file_handlers[ext](position=scenePos, auto_focus=False, filename=fn)
self.centerOn(a.editorItem)
e.accept()
def getXMLAnnotations(self, root):
# Iterate over the entire set (in order) creating a XML representation of the MatchDef and Style
for annotation in self.annotations:
ase = et.SubElement(root, "Annotation")
ase.set('type', type(annotation).__name__)
ase.set('x', str(annotation.x()))
ase.set('y', str(annotation.y()))
ase.set('width', str(annotation.rect().width()))
ase.set('height', str(annotation.rect().height()))
if hasattr(annotation, 'text'):
text = et.SubElement(ase, "Text")
text.text = annotation.text.toPlainText()
ase = annotation.config.getXMLConfig(ase)
return root
def setXMLAnnotations(self, root):
ANNOTATION_TYPES = {
'AnnotationTextItem': AnnotationTextItem,
'AnnotationRegionItem': AnnotationRegionItem,
}
for ase in root.findall('Annotation'):
# Validate the class definition before creating it
if ase.get('type') in ANNOTATION_TYPES:
pos = QPointF(float(ase.get('x')), float(ase.get('y')))
aobj = ANNOTATION_TYPES[ase.get('type')](position=pos)
aobj.setRect(QRectF(0, 0, float(ase.get('width')), float(ase.get('height'))))
to = ase.find('Text')
if to is not None:
aobj.text.setPlainText(to.text)
self.addItem(aobj)
self.annotations.append(aobj)
aobj.config.setXMLConfig(ase)
aobj.applyStyleConfig()
class MetaboHunter(GenericDialog):
options = {
'Metabotype': {
'All': 'All',
'Drug': 'Drug',
'Food additive': 'Food additive',
'Mammalian': 'Mammalian',
'Microbial': 'Microbial',
'Plant': 'Plant',
'Synthetic/Industrial chemical': 'Synthetic/Industrial chemical',
},
'Database Source': {
'Human Metabolome Database (HMDB)': 'HMDB',
'Madison Metabolomics Consortium Database (MMCD)': 'MMCD',
},
'Sample pH': {
'10.00 - 10.99': 'ph7',
'7.00 - 9.99': 'ph7',
'6.00 - 6.99': 'ph6',
'5.00 - 5.99': 'ph5',
'4.00 - 4.99': 'ph4',
'3.00 - 3.99': 'ph3',
},
'Solvent': {
'All': 'all',
'Water': 'water',
'CDCl3': 'cdcl3',
'CD3OD': '5d3od',
'5% DMSO': '5dmso',
},
'Frequency': {
'All': 'all',
'600 MHz': '600',
'500 MHz': '500',
'400 MHz': '400',
},
'Method': {
'MH1: Highest number of matched peaks':
'HighestNumber',
'MH2: Highest number of matched peaks with shift tolerance':
'HighestNumberNeighbourhood',
'MH3: Greedy selection of metabolites with disjoint peaks':
'Greedy2',
'MH4: Highest number of matched peaks with intensities':
'HighestNumberHeights',
'MH5: Greedy selection of metabolites with disjoint peaks and heights':
'Greedy2Heights',
},
}
def __init__(self, *args, **kwargs):
super(MetaboHunter, self).__init__(*args, **kwargs)
self.setWindowTitle('MetaboHunter')
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'Metabotype': 'All',
'Database Source': 'HMDB',
'Sample pH': 'ph7',
'Solvent': 'water',
'Frequency': 'all',
'Method': 'HighestNumberNeighbourhood',
'Noise Threshold': 0.0001,
'Confidence Threshold': 0.5,
'Tolerance': 0.1,
'convert_hmdb_ids_to_names': True,
})
self.lw_combos = {}
for o in [
'Metabotype', 'Database Source', 'Sample pH', 'Solvent',
'Frequency', 'Method'
]:
row = QVBoxLayout()
cl = QLabel(o)
cb = QComboBox()
cb.addItems(list(self.options[o].keys()))
row.addWidget(cl)
row.addWidget(cb)
self.config.add_handler(o, cb, self.options[o])
self.layout.addLayout(row)
row = QGridLayout()
self.lw_spin = {}
for n, o in enumerate(
['Noise Threshold', 'Confidence Threshold', 'Tolerance']):
cl = QLabel(o)
cb = QDoubleSpinBox()
cb.setDecimals(4)
cb.setRange(0, 1)
cb.setSingleStep(0.01)
cb.setValue(float(self.config.get(o)))
row.addWidget(cl, 0, n)
row.addWidget(cb, 1, n)
self.config.add_handler(o, cb)
self.layout.addLayout(row)
row = QHBoxLayout()
row.addWidget(QLabel("Convert HMDB IDs to chemical names?"))
conv = QCheckBox()
self.config.add_handler('convert_hmdb_ids_to_names', conv)
row.addWidget(conv)
self.layout.addLayout(row)
self.dialogFinalise()
class AnnotateClasses(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotateClasses, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Classes')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Sample classes')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_classes = QListWidgetAddRemove()
self.lw_classes.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_classes)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_class = QLineEdit()
addc = QPushButton('Add')
addc.clicked.connect(self.onClassAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onClassAdd)
loadc = QPushButton('Import from file')
loadc.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'folder-open-document.png')))
loadc.clicked.connect(self.onClassImport)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_class)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vboxh.addWidget(loadc)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/sample_classes', self.lw_classes,
(self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onClassAdd(self):
c = self.config.get(
'annotation/sample_classes'
)[:] # Create new list to force refresh on reassign
c.append((self.add_label.text(), self.add_class.text()))
self.config.set('annotation/sample_classes', c)
def onClassRemove(self):
i = self.lw_classes.removeItemAt(self.lw_classes.currentRow())
# c = self.map_list_fwd(i.text())
def onClassImport(self):
filename, _ = QFileDialog.getOpenFileName(
self.parent(), 'Load classifications from file', '',
"All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)"
)
if filename:
c = self.config.get(
'annotation/sample_classes'
)[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append(row[:2])
self.config.set('annotation/sample_classes', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%s" % tuple(x)
self.fwd_map_cache[s] = x
return s
class ToolBase(QObject):
'''
Base tool definition for inclusion in the UI. Define specific config settings;
attach a panel widget for configuration.
'''
is_manual_runnable = True
is_auto_runnable = False
is_auto_rerunnable = True
is_disableable = True
progress = pyqtSignal(float)
status = pyqtSignal(str)
complete = pyqtSignal()
config_panel_size = 150
view = None
def __init__(self, parent, *args, **kwargs):
super(ToolBase, self).__init__(parent, *args, **kwargs)
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'auto_run_on_config_change': True
})
self.current_status = 'inactive'
self.config.updated.connect(self.auto_run_on_config_change)
self.buttonBar = QWidget()
self.configPanels = QWidget()
self.configLayout = QVBoxLayout()
self.configLayout.setContentsMargins(0,0,0,0)
self.configPanels.setLayout(self.configLayout)
self._previous_config_backup_ = {}
self._worker_thread_ = None
self._worker_thread_lock_ = False
self.view = MplView(self.parent())
self.setup()
self.current_progress = 0
self.progress.connect(self.progress_callback)
self.status.connect(self.status_callback)
def setup(self):
self.data = {
'data': None,
}
self.view.figure.clear()
self.view.redraw()
self.status.emit('inactive' if self.current_status == 'inactive' else 'ready')
def addConfigPanel(self, panel):
self.configLayout.addWidget( panel(self) )
def addButtonBar(self, buttons):
'''
Create a button bar
Supplied with a list of QPushButton objects (already created using helper stubs; see below)
:param buttons:
:return:
'''
btnlayout = QHBoxLayout()
btnlayout.addSpacerItem(QSpacerItem(250, 1, QSizePolicy.Maximum, QSizePolicy.Maximum))
for btn in buttons:
btnlayout.addWidget(btn)
self.configLayout.addLayout(btnlayout)
btnlayout.addSpacerItem(QSpacerItem(250, 1, QSizePolicy.Maximum, QSizePolicy.Maximum))
def run_manual(self):
pass
def disable(self):
self.status.emit('inactive')
self.item.setFlags(Qt.NoItemFlags)
def reset(self):
self.config.set_many( self.config.defaults )
def undo(self):
self.config.set_many(self._config_backup_)
def defaultButtons(self):
buttons = []
reset = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'arrow-turn-180-left.png')), 'Reset to defaults')
reset.setToolTip('Reset to defaults')
reset.pressed.connect(self.reset)
buttons.append(reset)
apply = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'play.png')), 'Apply')
apply.setToolTip('Apply current settings to spectra')
apply.pressed.connect(self.run_manual)
buttons.append(apply)
return buttons
def enable(self):
if self.current_status == 'inactive':
self.current_status = 'ready'
self.status.emit('ready')
self.item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable)
def activate(self):
self.parent().current_tool = self
self.enable()
self._config_backup_ = self.config.as_dict()
self._refresh_plot_timer_ = QTimer.singleShot(0, self.plot)
if self.view:
self.parent().viewStack.setCurrentWidget(self.view)
self.parent().configstack.setCurrentWidget(self.configPanels)
self.parent().configstack.setMaximumHeight(self.config_panel_size)
def set_active(self, active):
self.config.set('is_active', active)
def get_previous_tool(self):
# Get the previous ACTIVE tool in the tool table
n = self.parent().tools.index(self)
for tool in self.parent().tools[n-1::-1]:
if tool.current_status != 'inactive':
return tool
else:
return None
def get_next_tool(self):
# Get the previous ACTIVE tool in the tool table
n = self.parent().tools.index(self)
for tool in self.parent().tools[n+1:]:
if tool.current_status != 'inactive':
return tool
else:
return None
def get_previous_data(self):
t = self.get_previous_tool()
if t and 'data' in t.data:
return t.data['data']
else:
return None
def plot(self, **kwargs):
pass
#if 'spc' in self.data:
# self.parent().spectraViewer.plot(self.data['spc'], **kwargs)
def get_plotitem(self):
return self.parent().spectraViewer.spectraViewer.plotItem
def auto_run_on_config_change(self):
if self.is_auto_runnable and self.current_status == 'ready' and self.config.get('auto_run_on_config_change'):
self.run_manual()
def run(self, fn):
'''
Run the target function, passing in the current spectra, and config settings (as dict)
:param fn:
:return:
'''
if self._worker_thread_lock_:
return False # Can't run
self.progress.emit(0)
self.status.emit('active')
data = self.get_previous_data()
self._worker_thread_lock_ = True
kwargs = {
'config': self.config.as_dict(),
'progress_callback': self.progress.emit,
}
if data:
kwargs.update(deepcopy(data))
# Close any open figures; ensure new axes.
plt.close()
self._worker_thread_ = Worker(fn = fn, **kwargs)
self._worker_thread_.signals.finished.connect(self.finished)
self._worker_thread_.signals.result.connect(self.result)
self._worker_thread_.signals.error.connect(self.error)
self.parent().threadpool.start(self._worker_thread_)
def error(self, error):
self.progress.emit(1.0)
self.status.emit('error')
logging.error(error)
self._worker_thread_lock_ = False
def result(self, result):
# Apply post-processing
if 'fig' in result and result['fig']:
fig = result['fig']
fig.set_size_inches(self.view.get_size_inches(fig.get_dpi()))
fig.set_tight_layout(False)
fig.tight_layout(pad=0.5, rect=[0.25, 0.10, 0.75, 0.90])
self.view.figure = fig
self.view.redraw()
self.data = result
self.plot()
self.progress.emit(1)
self.status.emit('complete')
def finished(self):
# Cleanup
self._worker_thread_lock_ = False
self.complete.emit()
def progress_callback(self, progress):
self.current_progress = progress
self.item.setData(Qt.UserRole + 2, progress)
def status_callback(self, status):
self.current_status = status
self.item.setData(Qt.UserRole + 3, status)
class QGraphicsSceneExtend(QGraphicsScene):
def __init__(self, parent, *args, **kwargs):
super(QGraphicsSceneExtend, self).__init__(parent, *args, **kwargs)
self.m = parent.m
self.config = ConfigManager()
# These config settings are transient (ie. not stored between sessions)
self.config.set_defaults({
'mode': EDITOR_MODE_NORMAL,
'font-family': 'Arial',
'font-size': '12',
'text-bold': False,
'text-italic': False,
'text-underline': False,
'text-color': '#000000',
'color-border': None, # '#000000',
'color-background': None,
})
# Pre-set these values (will be used by default)
self.config.set('color-background', '#5555ff')
self.background_image = QImage(
os.path.join(utils.scriptdir, 'icons', 'grid100.png'))
if settings.get('Editor/Show_grid'):
self.showGrid()
else:
self.hideGrid()
self.mode = EDITOR_MODE_NORMAL
self.mode_current_object = None
self.annotations = []
def mousePressEvent(self, e):
if self.config.get('mode') != EDITOR_MODE_NORMAL:
for i in self.selectedItems():
i.setSelected(False)
if self.config.get('mode') == EDITOR_MODE_TEXT:
tw = AnnotationTextItem(position=e.scenePos())
elif self.config.get('mode') == EDITOR_MODE_REGION:
tw = AnnotationRegionItem(position=e.scenePos())
elif self.config.get('mode') == EDITOR_MODE_ARROW:
tw = AnnotationRegionItem(position=e.scenePos())
self.addItem(tw)
self.mode_current_object = tw
tw._createFromMousePressEvent(e)
tw.importStyleConfig(self.config)
self.annotations.append(tw)
else:
super(QGraphicsSceneExtend, self).mousePressEvent(e)
def mouseMoveEvent(self, e):
if self.config.get(
'mode') == EDITOR_MODE_TEXT and self.mode_current_object:
self.mode_current_object._resizeFromMouseMoveEvent(e)
elif self.config.get(
'mode') == EDITOR_MODE_REGION and self.mode_current_object:
self.mode_current_object._resizeFromMouseMoveEvent(e)
else:
super(QGraphicsSceneExtend, self).mouseMoveEvent(e)
def mouseReleaseEvent(self, e):
if self.config.get('mode'):
self.mode_current_object.setSelected(True)
self.mode_current_object.setFocus()
self.config.set('mode', EDITOR_MODE_NORMAL)
self.mode_current_object = None
super(QGraphicsSceneExtend, self).mouseReleaseEvent(e)
def showGrid(self):
self.setBackgroundBrush(QBrush(self.background_image))
def hideGrid(self):
self.setBackgroundBrush(QBrush(None))
def onSaveAsImage(self):
filename, _ = QFileDialog.getSaveFileName(
self.m, 'Save current figure', '',
"Tagged Image File Format (*.tif);;\
Portable Network Graphics (*.png)"
)
if filename:
self.saveAsImage(filename)
def saveAsImage(self, f):
self.image = QImage(self.sceneRect().size().toSize(),
QImage.Format_ARGB32)
self.image.fill(Qt.white)
painter = QPainter(self.image)
self.render(painter)
self.image.save(f)
def addApp(self, app, position=None):
i = ToolItem(self, app, position=position)
self.addItem(i)
return i
def removeApp(self, app):
i = app.editorItem
i.hide()
self.removeItem(i)
app.editorItem = None
def dragEnterEvent(self, e):
if e.mimeData().hasFormat('application/x-pathomx-app') or e.mimeData(
).hasFormat('text/uri-list'):
e.accept()
else:
e.ignore()
def dragMoveEvent(self, e):
e.accept()
def dropEvent(self, e):
scenePos = e.scenePos() - QPointF(32, 32)
if e.mimeData().hasFormat('application/x-pathomx-app'):
try:
app_id = str(e.mimeData().data('application/x-pathomx-app'),
'utf-8') # Python 3
except:
app_id = str(
e.mimeData().data('application/x-pathomx-app')) # Python 2
e.setDropAction(Qt.CopyAction)
a = app_launchers[app_id](self.m,
position=scenePos,
auto_focus=False)
#self.centerOn(a.editorItem)
e.accept()
elif e.mimeData().hasFormat('text/uri-list'):
for ufn in e.mimeData().urls():
fn = ufn.path()
fnn, ext = os.path.splitext(fn)
ext = ext.strip('.')
if ext in file_handlers:
a = file_handlers[ext](position=scenePos,
auto_focus=False,
filename=fn)
self.centerOn(a.editorItem)
e.accept()
def getXMLAnnotations(self, root):
# Iterate over the entire set (in order) creating a XML representation of the MatchDef and Style
for annotation in self.annotations:
ase = et.SubElement(root, "Annotation")
ase.set('type', type(annotation).__name__)
ase.set('x', str(annotation.x()))
ase.set('y', str(annotation.y()))
ase.set('width', str(annotation.rect().width()))
ase.set('height', str(annotation.rect().height()))
if hasattr(annotation, 'text'):
text = et.SubElement(ase, "Text")
text.text = annotation.text.toPlainText()
ase = annotation.config.getXMLConfig(ase)
return root
def setXMLAnnotations(self, root):
ANNOTATION_TYPES = {
'AnnotationTextItem': AnnotationTextItem,
'AnnotationRegionItem': AnnotationRegionItem,
}
for ase in root.findall('Annotation'):
# Validate the class definition before creating it
if ase.get('type') in ANNOTATION_TYPES:
pos = QPointF(float(ase.get('x')), float(ase.get('y')))
aobj = ANNOTATION_TYPES[ase.get('type')](position=pos)
aobj.setRect(
QRectF(0, 0, float(ase.get('width')),
float(ase.get('height'))))
to = ase.find('Text')
if to is not None:
aobj.text.setPlainText(to.text)
self.addItem(aobj)
self.annotations.append(aobj)
aobj.config.setXMLConfig(ase)
aobj.applyStyleConfig()
class Automaton(QStandardItem):
def __init__(self, *args, **kwargs):
super(Automaton, self).__init__(*args, **kwargs)
self.setData(self, Qt.UserRole)
self.watcher = QFileSystemWatcher()
self.timer = QTimer()
self.watch_window = {}
self.latest_run = {}
self.is_running = False
self.config = ConfigManager()
self.config.set_defaults({
'mode': MODE_WATCH_FOLDER,
'is_active': True,
'trigger_hold': 1,
'notebook_paths': '',
'output_path': '{home}/{notebook_filename}_{datetime}_',
'output_format': 'html',
'watched_files': [],
'watched_folder': '',
'watch_window': 15,
'iterate_watched_folder': True,
'iterate_wildcard': '.csv',
'timer_seconds': 60,
})
self.runner = None
self.lock = None
self.latest_run = {
'timestamp': None,
'success': None,
}
# Set up all the triggers
self.watcher.fileChanged.connect(self.file_trigger_accumulator)
self.watcher.directoryChanged.connect(self.trigger)
self.timer.timeout.connect(self.trigger)
def startup(self):
if self.config.get('is_active') == False:
return False
if self.config.get('mode') == MODE_TIMER:
self.timer.setInterval(self.config.get('timer_seconds') * 1000)
self.timer.start()
elif self.config.get('mode') == MODE_WATCH_FILES:
current_paths = self.watcher.files() + self.watcher.directories()
if current_paths:
self.watcher.removePaths(current_paths)
self.watch_window = {}
self.watcher.addPaths(self.config.get('watched_files'))
elif self.config.get('mode') == MODE_WATCH_FOLDER:
current_paths = self.watcher.files() + self.watcher.directories()
if current_paths:
self.watcher.removePaths(current_paths)
self.watcher.addPath(self.config.get('watched_folder'))
def shutdown(self):
if self.config.get('mode') == MODE_TIMER:
self.timer.stop()
elif self.config.get('mode') == MODE_WATCH_FILES or self.config.get(
'mode') == MODE_WATCH_FOLDER:
current_paths = self.watcher.files() + self.watcher.directories()
if current_paths:
self.watcher.removePaths(current_paths)
self.watch_window = {}
def load_notebook(self, filename):
try:
with open(filename) as f:
nb = reads(f.read(), 'json')
except:
return None
else:
return nb
def file_trigger_accumulator(self, f):
# Accumulate triggers from changed files: if 3 files are specified to watch
# we only want to fire once _all_ files have changed (within the given watch window)
current_time = datetime.now()
self.watch_window[f] = current_time # timestamp
self.watch_window = {
k: v
for k, v in self.watch_window.items() if current_time -
timedelta(seconds=self.config.get('watch_window')) < v
}
if set(self.watch_window.keys()) == set(self.watcher.files() +
self.watcher.directories()):
self.trigger()
def trigger(self, e=None):
if self.config.get('is_active') == False:
return False
# Filesystemwatcher triggered
# Get the file and folder information; make available in vars object for run
if self.lock is None:
self.is_running = True
self.update()
self.lock = QTimer.singleShot(
self.config.get('trigger_hold') * 1000, self.run)
# Shutdown so we don't get in infinite loops
self.shutdown()
def run(self, vars={}):
default_vars = {
'home': os.path.expanduser('~'),
'version': VERSION_STRING,
}
default_vars_and_config = dict(
list(default_vars.items()) + list(self.config.config.items()))
if self.runner == None:
# Postpone init to trigger for responsiveness on add/remove
self.runner = NotebookRunner(None, pylab=True, mpl_inline=True)
if self.config.get('mode') == MODE_WATCH_FOLDER and self.config.get(
'iterate_watched_folder'):
for (dirpath, dirnames,
filenames) in os.walk(self.config.get('watched_folder')):
break
filenames = [
f for f in filenames
if self.config.get('iterate_wildcard') in f
]
logging.info('Watched folder contains %d files; looping' %
len(filenames))
# Filenames contains the list of files in the folder
else:
filenames = [None]
self.latest_run['timestamp'] = datetime.now()
try:
for f in filenames:
now = datetime.now()
current_vars = {
'datetime': now.strftime("%Y-%m-%d %H.%M.%S"),
'date': now.date().strftime("%Y-%m-%d"),
'time': now.time().strftime("%H.%M.%S"),
'filename': f,
}
vars = dict(
list(default_vars_and_config.items()) +
list(current_vars.items()))
for nb_path in self.config.get('notebook_paths'):
nb = self.load_notebook(nb_path)
if nb:
# Add currently running notebook path to vars
vars['notebook_path'] = nb_path
vars['notebook_filename'] = os.path.basename(nb_path)
vars['output_path'] = self.config.get(
'output_path').format(**vars)
parent_folder = os.path.dirname(vars['output_path'])
if parent_folder:
try:
utils.mkdir_p(parent_folder)
except: # Can't create folder
self.latest_run['success'] = False
raise
self.run_notebook(nb, vars)
else:
raise NotebookNotFound(nb_path)
except:
self.latest_run['success'] = False
traceback.print_exc()
exctype, value = sys.exc_info()[:2]
logging.error("%s\n%s\n%s" %
(exctype, value, traceback.format_exc()))
finally:
self.is_running = False
self.lock = None
self.update()
# Restart
self.startup()
def run_notebook(self, nb, vars={}):
if len(nb['worksheets']) == 0:
nb['worksheets'] = [NotebookNode({'cells': [], 'metadata': {}})]
start = nb['worksheets'][0]['cells']
start.insert(
0,
Struct(
**{
'cell_type': 'code',
'language': 'python',
'outputs': [],
'collapsed': False,
'prompt_number': -1,
'input': 'qtipy=%s' % vars,
'metadata': {},
}))
self.runner.nb = nb
try:
self.runner.run_notebook()
except:
self.latest_run['success'] = False
raise
else:
self.latest_run['success'] = True
finally:
ext = dict(
html='html',
slides='slides',
latex='latex',
markdown='md',
python='py',
rst='rst',
)
output, resources = IPyexport(
IPyexporter_map[self.config.get('output_format')],
self.runner.nb)
output_path = vars['output_path'] + 'notebook.%s' % ext[
self.config.get('output_format')]
logging.info("Exporting updated notebook to %s" % output_path)
with open(output_path, "w") as f:
f.write(output)
def update(self):
global _w
_w.viewer.update(self.index())
class Automaton(QStandardItem):
def __init__(self, *args, **kwargs):
super(Automaton, self).__init__(*args, **kwargs)
self.setData(self, Qt.UserRole)
self.watcher = QFileSystemWatcher()
self.timer = QTimer()
self.watch_window = {}
self.latest_run = {}
self.is_running = False
self.config = ConfigManager()
self.config.set_defaults({
'mode': MODE_WATCH_FOLDER,
'is_active': True,
'trigger_hold': 1,
'notebook_paths': '',
'output_path': '{home}/{notebook_filename}_{datetime}_',
'output_format': 'html',
'watched_files': [],
'watched_folder': '',
'watch_window': 15,
'iterate_watched_folder': True,
'iterate_wildcard': '.csv',
'timer_seconds': 60,
})
self.runner = None
self.lock = None
self.latest_run = {
'timestamp': None,
'success': None,
}
# Set up all the triggers
self.watcher.fileChanged.connect(self.file_trigger_accumulator)
self.watcher.directoryChanged.connect(self.trigger)
self.timer.timeout.connect(self.trigger)
def startup(self):
if self.config.get('is_active') == False:
return False
if self.config.get('mode') == MODE_TIMER:
self.timer.setInterval(self.config.get('timer_seconds') * 1000)
self.timer.start()
elif self.config.get('mode') == MODE_WATCH_FILES:
current_paths = self.watcher.files() + self.watcher.directories()
if current_paths:
self.watcher.removePaths(current_paths)
self.watch_window = {}
self.watcher.addPaths(self.config.get('watched_files'))
elif self.config.get('mode') == MODE_WATCH_FOLDER:
current_paths = self.watcher.files() + self.watcher.directories()
if current_paths:
self.watcher.removePaths(current_paths)
self.watcher.addPath(self.config.get('watched_folder'))
def shutdown(self):
if self.config.get('mode') == MODE_TIMER:
self.timer.stop()
elif self.config.get('mode') == MODE_WATCH_FILES or self.config.get('mode') == MODE_WATCH_FOLDER:
current_paths = self.watcher.files() + self.watcher.directories()
if current_paths:
self.watcher.removePaths(current_paths)
self.watch_window = {}
def load_notebook(self, filename):
try:
with open(filename) as f:
nb = reads(f.read(), 'json')
except:
return None
else:
return nb
def file_trigger_accumulator(self, f):
# Accumulate triggers from changed files: if 3 files are specified to watch
# we only want to fire once _all_ files have changed (within the given watch window)
current_time = datetime.now()
self.watch_window[f] = current_time # timestamp
self.watch_window = {k: v for k, v in self.watch_window.items() if current_time - timedelta(seconds=self.config.get('watch_window')) < v}
if set(self.watch_window.keys()) == set(self.watcher.files() + self.watcher.directories()):
self.trigger()
def trigger(self, e=None):
if self.config.get('is_active') == False:
return False
# Filesystemwatcher triggered
# Get the file and folder information; make available in vars object for run
if self.lock is None:
self.is_running = True
self.update()
self.lock = QTimer.singleShot(self.config.get('trigger_hold') * 1000, self.run)
# Shutdown so we don't get in infinite loops
self.shutdown()
def run(self, vars={}):
default_vars = {
'home': os.path.expanduser('~'),
'version': VERSION_STRING,
}
default_vars_and_config = dict(list(default_vars.items()) + list(self.config.config.items()))
if self.runner == None:
# Postpone init to trigger for responsiveness on add/remove
self.runner = NotebookRunner(None, pylab=True, mpl_inline=True)
if self.config.get('mode') == MODE_WATCH_FOLDER and self.config.get('iterate_watched_folder'):
for (dirpath, dirnames, filenames) in os.walk(self.config.get('watched_folder')):
break
filenames = [f for f in filenames if self.config.get('iterate_wildcard') in f]
logging.info('Watched folder contains %d files; looping' % len(filenames))
# Filenames contains the list of files in the folder
else:
filenames = [None]
self.latest_run['timestamp'] = datetime.now()
try:
for f in filenames:
now = datetime.now()
current_vars = {
'datetime': now.strftime("%Y-%m-%d %H.%M.%S"),
'date': now.date().strftime("%Y-%m-%d"),
'time': now.time().strftime("%H.%M.%S"),
'filename': f,
}
vars = dict(list(default_vars_and_config.items()) + list(current_vars.items()))
for nb_path in self.config.get('notebook_paths'):
nb = self.load_notebook(nb_path)
if nb:
# Add currently running notebook path to vars
vars['notebook_path'] = nb_path
vars['notebook_filename'] = os.path.basename(nb_path)
vars['output_path'] = self.config.get('output_path').format(**vars)
parent_folder = os.path.dirname(vars['output_path'])
if parent_folder:
try:
utils.mkdir_p(parent_folder)
except: # Can't create folder
self.latest_run['success'] = False
raise
self.run_notebook(nb, vars)
else:
raise NotebookNotFound(nb_path)
except:
self.latest_run['success'] = False
traceback.print_exc()
exctype, value = sys.exc_info()[:2]
logging.error("%s\n%s\n%s" % (exctype, value, traceback.format_exc()))
finally:
self.is_running = False
self.lock = None
self.update()
# Restart
self.startup()
def run_notebook(self, nb, vars={}):
if len(nb['worksheets']) == 0:
nb['worksheets'] = [NotebookNode({'cells': [], 'metadata': {}})]
start = nb['worksheets'][0]['cells']
start.insert(0, Struct(**{
'cell_type': 'code',
'language': 'python',
'outputs': [],
'collapsed': False,
'prompt_number': -1,
'input': 'qtipy=%s' % vars,
'metadata': {},
}))
self.runner.nb = nb
try:
self.runner.run_notebook()
except:
self.latest_run['success'] = False
raise
else:
self.latest_run['success'] = True
finally:
ext = dict(
html='html',
slides='slides',
latex='latex',
markdown='md',
python='py',
rst='rst',
)
output, resources = IPyexport(IPyexporter_map[self.config.get('output_format')], self.runner.nb)
output_path = vars['output_path'] + 'notebook.%s' % ext[self.config.get('output_format')]
logging.info("Exporting updated notebook to %s" % output_path)
with open(output_path, "w") as f:
f.write(output)
def update(self):
global _w
_w.viewer.update(self.index())
class AnnotatePeaks(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotatePeaks, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Peaks')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Peaks')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_peaks = QListWidgetAddRemove()
self.lw_peaks.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_peaks)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_start = QDoubleSpinBox()
self.add_start.setRange(-1, 12)
self.add_start.setDecimals(3)
self.add_start.setSuffix('ppm')
self.add_start.setSingleStep(0.001)
self.add_end = QDoubleSpinBox()
self.add_end.setRange(-1, 12)
self.add_end.setDecimals(3)
self.add_end.setSuffix('ppm')
self.add_end.setSingleStep(0.001)
addc = QPushButton('Add')
addc.clicked.connect(self.onPeakAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onPeakAdd)
loadc = QPushButton("Import from file")
loadc.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'folder-open-document.png')))
loadc.clicked.connect(self.onPeakImport)
metabh = QPushButton("Auto match via MetaboHunter")
metabh.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'metabohunter.png')))
metabh.clicked.connect(self.onPeakImportMetabohunter)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_start)
vboxh.addWidget(self.add_end)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vbox.addWidget(loadc)
vbox.addWidget(metabh)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/peaks', self.lw_peaks, (self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onPeakAdd(self):
c = self.config.get('annotation/peaks')[:] # Create new list to force refresh on reassign
c.append( (self.add_label.text(), float(self.add_start.value()), float(self.add_end.value()) ) )
self.config.set('annotation/peaks', c)
def onPeakRemove(self):
i = self.lw_peaks.removeItemAt(self.lw_peaks.currentRow())
# c = self.map_list_fwd(i.text())
def onPeakImport(self):
filename, _ = QFileDialog.getOpenFileName(self.parent(), 'Load peak annotations from file', '', "All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)")
if filename:
c = self.config.get('annotation/peaks')[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append( row[0], float(row[1]), float(row[2]) )
self.config.set('annotation/peaks', c)
def onPeakImportMetabohunter(self):
c = self.config.get('annotation/peaks')[:] # Create new list to force refresh on reassign
t = self.parent().current_tool
dlg = MetaboHunter(self)
if dlg.exec_():
if 'spc' in t.data:
# We have a spectra; calcuate mean; reduce size if required
spc = t.data['spc']
n = spc.data.shape[1]
ppm = spc.ppm
spcd = np.mean(spc.data, axis=0)
# Set a hard limit on the size of data we submit to be nice.
if n > 3000:
# Calculate the division required to be under the limit
d = np.ceil(float(n)/3000)
# Trim axis to multiple of divisor
trim = (n//d)*d
spcd = spcd[:trim]
ppm = ppm[:trim]
# Mean d shape
spcd = np.mean( spcd.reshape(-1,d), axis=1)
ppm = np.mean( ppm.reshape(-1,d), axis=1)
# Submit with settings
hmdbs = metabohunter.request(ppm, spcd,
metabotype=dlg.config.get('Metabotype'),
database=dlg.config.get('Database Source'),
ph=dlg.config.get('Sample pH'),
solvent=dlg.config.get('Solvent'),
frequency=dlg.config.get('Frequency'),
method=dlg.config.get('Method'),
noise=dlg.config.get('Noise Threshold'),
confidence=dlg.config.get('Confidence Threshold'),
tolerance=dlg.config.get('Tolerance')
)
ha = np.array(hmdbs)
unique_hmdbs = set(hmdbs)
if None in unique_hmdbs:
unique_hmdbs.remove(None)
# Extract out regions
for hmdb in unique_hmdbs:
hb = np.diff(ha == hmdb)
# These are needed to ensure markers are there for objects starting and ending on array edge
if ha[0] == hmdb:
hb[0] == True
if ha[-1] == hmdb:
hb[-1] == True
idx = np.nonzero(hb)[0]
idx = idx.reshape(-1,2)
if dlg.config.get('convert_hmdb_ids_to_names') and hmdb in METABOHUNTER_HMDB_NAME_MAP.keys():
label = METABOHUNTER_HMDB_NAME_MAP[hmdb]
else:
label = hmdb
# Now we have an array of all start, stop positions for this item
for start, stop in idx:
c.append( (label, ppm[start], ppm[stop]) )
self.config.set('annotation/peaks', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%.2f\t%.2f" % tuple(x)
self.fwd_map_cache[s] = x
return s
class AnnotateClasses(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotateClasses, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Classes')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Sample classes')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_classes = QListWidgetAddRemove()
self.lw_classes.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_classes)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_class = QLineEdit()
addc = QPushButton('Add')
addc.clicked.connect(self.onClassAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onClassAdd)
loadc = QPushButton('Import from file')
loadc.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'folder-open-document.png')))
loadc.clicked.connect(self.onClassImport)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_class)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vboxh.addWidget(loadc)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/sample_classes', self.lw_classes, (self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onClassAdd(self):
c = self.config.get('annotation/sample_classes')[:] # Create new list to force refresh on reassign
c.append( (self.add_label.text(), self.add_class.text()) )
self.config.set('annotation/sample_classes', c)
def onClassRemove(self):
i = self.lw_classes.removeItemAt(self.lw_classes.currentRow())
# c = self.map_list_fwd(i.text())
def onClassImport(self):
filename, _ = QFileDialog.getOpenFileName(self.parent(), 'Load classifications from file', '', "All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)")
if filename:
c = self.config.get('annotation/sample_classes')[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append(row[:2])
self.config.set('annotation/sample_classes', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%s" % tuple(x)
self.fwd_map_cache[s] = x
return s
class MetaboHunter(GenericDialog):
options = {
'Metabotype': {
'All': 'All',
'Drug': 'Drug',
'Food additive': 'Food additive',
'Mammalian': 'Mammalian',
'Microbial': 'Microbial',
'Plant': 'Plant',
'Synthetic/Industrial chemical': 'Synthetic/Industrial chemical',
},
'Database Source': {
'Human Metabolome Database (HMDB)': 'HMDB',
'Madison Metabolomics Consortium Database (MMCD)': 'MMCD',
},
'Sample pH': {
'10.00 - 10.99': 'ph7',
'7.00 - 9.99': 'ph7',
'6.00 - 6.99': 'ph6',
'5.00 - 5.99': 'ph5',
'4.00 - 4.99': 'ph4',
'3.00 - 3.99': 'ph3',
},
'Solvent': {
'All': 'all',
'Water': 'water',
'CDCl3': 'cdcl3',
'CD3OD': '5d3od',
'5% DMSO': '5dmso',
},
'Frequency': {
'All': 'all',
'600 MHz': '600',
'500 MHz': '500',
'400 MHz': '400',
},
'Method': {
'MH1: Highest number of matched peaks': 'HighestNumber',
'MH2: Highest number of matched peaks with shift tolerance': 'HighestNumberNeighbourhood',
'MH3: Greedy selection of metabolites with disjoint peaks': 'Greedy2',
'MH4: Highest number of matched peaks with intensities': 'HighestNumberHeights',
'MH5: Greedy selection of metabolites with disjoint peaks and heights': 'Greedy2Heights',
},
}
def __init__(self, *args, **kwargs):
super(MetaboHunter, self).__init__(*args, **kwargs)
self.setWindowTitle('MetaboHunter')
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'Metabotype': 'All',
'Database Source': 'HMDB',
'Sample pH': 'ph7',
'Solvent': 'water',
'Frequency': 'all',
'Method': 'HighestNumberNeighbourhood',
'Noise Threshold': 0.0001,
'Confidence Threshold': 0.5,
'Tolerance': 0.1,
'convert_hmdb_ids_to_names': True,
})
self.lw_combos = {}
for o in ['Metabotype', 'Database Source', 'Sample pH', 'Solvent', 'Frequency', 'Method']:
row = QVBoxLayout()
cl = QLabel(o)
cb = QComboBox()
cb.addItems(list(self.options[o].keys()))
row.addWidget(cl)
row.addWidget(cb)
self.config.add_handler(o, cb, self.options[o])
self.layout.addLayout(row)
row = QGridLayout()
self.lw_spin = {}
for n, o in enumerate(['Noise Threshold', 'Confidence Threshold', 'Tolerance']):
cl = QLabel(o)
cb = QDoubleSpinBox()
cb.setDecimals(4)
cb.setRange(0, 1)
cb.setSingleStep(0.01)
cb.setValue(float(self.config.get(o)))
row.addWidget(cl, 0, n)
row.addWidget(cb, 1, n)
self.config.add_handler(o, cb)
self.layout.addLayout(row)
row = QHBoxLayout()
row.addWidget(QLabel("Convert HMDB IDs to chemical names?"))
conv = QCheckBox()
self.config.add_handler('convert_hmdb_ids_to_names', conv)
row.addWidget(conv)
self.layout.addLayout(row)
self.dialogFinalise()
