def export_data(self):
try:
item = self.ui.h5file_tree.ui.Tree.currentItem()
self.current_node_path = item.text(2)
node = self.h5file.get_node(item.text(2))
if 'ARRAY' in node._v_attrs['CLASS']:
data = node.read()
if isinstance(data, np.ndarray):
file = select_file(save=True, ext='txt')
if file != '':
np.savetxt(file, data, '%.6e', '\t')
elif 'GROUP' in node._v_attrs['CLASS']:
children_names = list(node._v_children)
data = []
header = []
for subnode_name in node._v_children:
subnode = node._f_get_child(subnode_name)
if 'ARRAY' in subnode._v_attrs['CLASS']:
if len(subnode.shape) == 1:
data.append(subnode.read())
header.append(subnode_name)
file = select_file(save=True, ext='txt')
if file != '':
np.savetxt(file,
np.array(data).T,
'%.6e',
'\t',
header='\t'.join(header))
except Exception as e:
self.status_signal.emit(getLineInfo() + str(e))
def load_file(self, base_path=None, file_path=None):
"""Opens a file dialog to select a h5file saved on disk to be used
Parameters
----------
base_path
file_path
See Also
--------
:py:meth:`init_file`
:py:meth:`pymodaq.daq_utils.daq_utils.select_file`
"""
if base_path is None:
base_path = self.settings.child('base_path').value()
if not os.path.isdir(base_path):
base_path = None
if file_path is None:
file_path = utils.select_file(base_path, save=False, ext='h5')
if not isinstance(file_path, Path):
file_path = Path(file_path)
if 'h5' not in file_path.suffix:
raise IOError('Invalid file type, should be a h5 file')
self.init_file(addhoc_file_path=file_path)
def __init__(self, msgbox=False):
self.preset_params = None
self.pid_type = False
if msgbox:
msgBox = QtWidgets.QMessageBox()
msgBox.setText("Preset Manager?")
msgBox.setInformativeText("What do you want to do?")
cancel_button = msgBox.addButton(QtWidgets.QMessageBox.Cancel)
new_button = msgBox.addButton("New",
QtWidgets.QMessageBox.ActionRole)
modify_button = msgBox.addButton('Modify',
QtWidgets.QMessageBox.AcceptRole)
msgBox.setDefaultButton(QtWidgets.QMessageBox.Cancel)
ret = msgBox.exec()
if msgBox.clickedButton() == new_button:
self.set_new_preset()
elif msgBox.clickedButton() == modify_button:
path = select_file(start_path=preset_path,
save=False,
ext='xml')
if path != '':
self.set_file_preset(str(path))
else: #cancel
pass
def load_data(self):
self.h5file_path = str(
utils.select_file(start_path=None, save=False, ext='h5'))
if self.h5file_path != '':
self.settings.child('settings',
'filepath').setValue(self.h5file_path)
if self.h5file is not None:
self.h5file.close()
self.h5file = tables.open_file(self.h5file_path, 'a')
self.list_2Dscans()
def load_file(self, h5file=None):
if h5file is None:
h5file = str(select_file(start_path=None, save=False, ext='h5'))
if isinstance(h5file, str) or isinstance(h5file, Path):
h5file = tables.open_file(str(h5file), 'a')
elif isinstance(h5file, tables.File):
pass
else:
raise Exception('not a valid h5 file or path to a h5 file')
self.h5file = h5file
self.populate_tree()
def save_ROI(self):
try:
data = custom_tree.parameter_to_xml_string(
self.settings.child(('ROIs')))
path = select_file(ext='roi')
if path != '':
with open(path, 'wb') as f:
f.write(data)
except Exception as e:
print(e)
def export_data(self):
try:
item = self.ui.h5file_tree.ui.Tree.currentItem()
self.current_node_path = item.text(2)
node = self.h5file.get_node(item.text(2))
if 'ARRAY' in node._v_attrs['CLASS']:
data = node.read()
if isinstance(data, np.ndarray):
file = select_file(save=True, ext='txt')
if file != '':
np.savetxt(file, data, '%.6e', '\t')
except Exception as e:
self.status_signal.emit(getLineInfo() + str(e))
def modify_shortcuts(self):
try:
path = select_file(start_path=shortcut_path, save=False, ext='xml')
if path != '':
self.shortcut_manager.set_file_preset(str(path))
mssg = QtWidgets.QMessageBox()
mssg.setText(
f'You have to restart the application to take the modifications into account! '
f'Quitting the application...')
mssg.exec()
self.quit_fun()
else: # cancel
pass
except Exception as e:
self.update_status(getLineInfo() + str(e))
def load_file(self, base_path=None, file_path=None):
if base_path is None:
base_path = self.settings.child('base_path').value()
if not os.path.isdir(base_path):
base_path = None
if file_path is None:
file_path = utils.select_file(base_path, save=False, ext='h5')
if not isinstance(file_path, Path):
file_path = Path(file_path)
if not file_path.suffix == 'h5':
raise IOError('Invalid file type, should be a h5 file')
self.init_file(addhoc_file_path=file_path)
def save_layout_state(self, file=None):
"""
Save the current layout state in the select_file obtained pathname file.
Once done dump the pickle.
See Also
--------
utils.select_file
"""
try:
dockstate = self.dockarea.saveState()
if file is None:
file = select_file(start_path=None, save=True, ext='dock')
if file is not None:
with open(str(file), 'wb') as f:
pickle.dump(dockstate, f, pickle.HIGHEST_PROTOCOL)
except:
pass
def save_data(self):
try:
path = utils.select_file(start_path=self.settings.child(
'main_settings', 'base_path').value(),
save=True,
ext='h5')
if path is not None:
#init the file object with an addhoc name given by the user
h5saver = H5Saver(save_type='custom')
h5saver.init_file(update_h5=True, addhoc_file_path=path)
#save all metadata
settings_str = custom_tree.parameter_to_xml_string(
self.settings)
settings_str = b'<All_settings>' + settings_str
settings_str += custom_tree.parameter_to_xml_string(self.detector.settings) + \
custom_tree.parameter_to_xml_string(h5saver.settings) + \
b'</All_settings>'
data_group = h5saver.add_data_group(
h5saver.raw_group,
group_data_type='data0D',
title='data from custom app',
settings_as_xml=settings_str)
for dat in self.raw_data:
channel = h5saver.add_CH_group(data_group)
data_dict = dict(data=np.array(dat),
x_axis=dict(data=np.linspace(
0,
len(dat) - 1, len(dat)),
units='pxl'))
h5saver.add_data(channel,
data_dict=data_dict,
scan_type='')
st = 'file {:s} has been saved'.format(str(path))
self.add_log(st)
self.settings.child('main_settings', 'info').setValue(st)
h5saver.close_file()
except Exception as e:
self.add_log(getLineInfo() + str(e))
def load_ROI(self, path=None):
try:
if path is None:
path = select_file(save=False, ext='roi')
if path != '':
for roi in self.ROIs.values():
index = roi.index
self.viewer_widget.plotitem.removeItem(roi)
#self.settings.sigTreeStateChanged.disconnect()
self.settings.child(*('ROIs',
'ROI_%02.0d' % index)).remove()
#self.settings.sigTreeStateChanged.connect(self.roi_tree_changed)
self.ROIs = OrderedDict([])
params = custom_tree.XML_file_to_parameter(path)
self.settings.child(('ROIs')).addChildren(params)
except Exception as e:
pass
def load_layout_state(self, file=None):
"""
Load and restore a layout state from the select_file obtained pathname file.
See Also
--------
utils.select_file
"""
try:
if file is None:
file = select_file(save=False, ext='dock')
if file is not None:
with open(str(file), 'rb') as f:
dockstate = pickle.load(f)
self.dockarea.restoreState(dockstate)
file = os.path.split(file)[1]
self.settings.child('loaded_files', 'layout_file').setValue(file)
except:
pass
def load_h5_file(self, path=None):
"""
| Load the specific h5 file calling the open_h5_file procedure
================ ============ =======================================
**Parameters** **Type** **Description**
*path* string the current path to the file to load
================ ============ =======================================
See Also
--------
open_h5_file, update_status, daq_utils.select_file
"""
try:
filename = select_file(start_path=path, save=False, ext='h5')
if filename is not "":
self.open_h5_file(filename)
except Exception as e:
self.update_status(str(e), wait_time=self.wait_time)
def save_data(self):
try:
fname = utils.select_file(start_path=self.save_file_pathname,
save=True,
ext='h5')
if not (not (fname)):
with tables.open_file(
str(fname), mode='w',
title='an example h5 file name') as h5file:
data_to_save = np.squeeze(np.array(self.raw_data))
#save metadata
h5file.root._v_attrs[
'settings'] = custom_tree.parameter_to_xml_string(
self.settings)
for ind in range(data_to_save.shape[1]):
arr = h5file.create_array('/', 'data_{:d}'.format(ind),
data_to_save[:, ind])
arr._v_attrs['shape'] = data_to_save.shape[0]
arr._v_attrs['type'] = 'data1D'
arr = h5file.create_array('/', 'data_2D', data_to_save)
arr._v_attrs['shape'] = data_to_save.shape
arr._v_attrs['type'] = 'data2D'
logger = "logging"
text_atom = tables.atom.ObjectAtom()
logger_array = h5file.create_vlarray('/',
logger,
atom=text_atom)
logger_array._v_attrs['type'] = 'list'
for ind_log in range(self.logger_list.count()):
txt = self.logger_list.item(ind_log).text()
logger_array.append(txt)
st = 'file {:s} has been saved'.format(fname)
self.add_log(st)
self.settings.child('min_settings', 'info').setValue(st)
except Exception as e:
self.add_log(str(e))
def __init__(self, parent, h5file=None):
QLocale.setDefault(QLocale(QLocale.English, QLocale.UnitedStates))
super(H5Browser, self).__init__()
if type(parent) is not QtWidgets.QWidget:
raise Exception('no valid parent container, expected a QWidget')
self.parent = parent
if h5file is None:
h5file = str(select_file(start_path=None, save=False, ext='h5'))
if type(h5file) == str:
h5file = tables.open_file(h5file, 'a')
elif type(h5file) == tables.File:
pass
else:
raise Exception('not a valid h5 file or path to a h5 file')
self.h5file = h5file
self.ui = QObject() #the user interface
self.set_GUI()
self.populate_tree()
self.ui.h5file_tree.ui.Open_Tree.click()
def init_file(self,
update_h5=False,
custom_naming=False,
addhoc_file_path=None):
"""
init a new h5 file. Could be a file with a given name (addhoc_file_path) or following the template for scans
(datasets) or for detectors or a box to set a custom name (custom naming)
Parameters
----------
update_h5: (bool) create a new h5 file with name specified by other parameters if false try to open an existing
file or create it if it doesn't exists
custom_naming: (bool) if True, a selection file dialog opens to set a new file name
addhoc_file_path: (Path) supplied name for the file
Returns
-------
bool: True if new file has been created, False otherwise
"""
date = datetime.datetime.now()
if addhoc_file_path is None:
if not os.path.isdir(self.settings.child(('base_path')).value()):
os.mkdir(self.settings.child(('base_path')).value())
# set the filename and path
base_name = self.settings.child(('base_name')).value()
if not custom_naming:
custom_naming = self.settings.child(('custom_name')).value()
if not custom_naming:
scan_type = self.settings.child(
('save_type')).value() == 'scan'
scan_path, current_scan_name, save_path = self.update_file_paths(
update_h5)
self.current_scan_name = current_scan_name
self.settings.child(
('current_scan_name')).setValue(current_scan_name)
self.settings.child(
('current_scan_path')).setValue(str(scan_path))
if not scan_type:
self.h5_file_path = save_path #will remove the dataset part used for DAQ_scan datas
self.h5_file_name = base_name + date.strftime(
'_%Y%m%d_%H_%M_%S.h5')
else:
self.h5_file_path = save_path
self.h5_file_name = save_path.name + ".h5"
else:
self.h5_file_name = utils.select_file(start_path=base_name,
save=True,
ext='h5')
self.h5_file_path = self.h5_file_name.parent
else:
if isinstance(addhoc_file_path, str):
addhoc_file_path = Path(addhoc_file_path)
self.h5_file_path = addhoc_file_path.parent
self.h5_file_name = addhoc_file_path.name
fullpathname = str(self.h5_file_path.joinpath(self.h5_file_name))
self.settings.child(('current_h5_file')).setValue(fullpathname)
if update_h5:
self.current_scan_group = None
scan_group = None
if self.current_scan_group is not None:
scan_group = self.current_scan_group._v_name
if update_h5:
self.close_file()
self.h5_file = tables.open_file(fullpathname,
'w',
title='PyMoDAQ file')
self.h5_file.root._v_attrs['pymodaq_version'] = get_version()
else:
self.close_file()
self.h5_file = tables.open_file(fullpathname,
'a',
title='PyMoDAQ file')
self.raw_group = self.get_set_group(self.h5_file.root,
'Raw_datas',
title='Data from PyMoDAQ modules')
self.get_set_logger(self.raw_group)
if scan_group is not None:
self.current_scan_group = self.get_set_group(
self.raw_group, scan_group)
else:
self.current_scan_group = self.get_last_scan()
self.raw_group._v_attrs['type'] = self.settings.child(
('save_type')).value()
self.h5_file.root._v_attrs['file'] = date.strftime(self.h5_file_name)
if update_h5:
self.h5_file.root._v_attrs['date'] = date.strftime('%Y%m%d')
self.h5_file.root._v_attrs['time'] = date.strftime('%H:%M:%S')
return update_h5
def save_file(self):
filename = select_file(None, save=True, ext='h5')
self.h5file.copy_file(str(filename))
def init_file(self,
update_h5=False,
custom_naming=False,
addhoc_file_path=None):
"""Initializes a new h5 file.
Could set the h5_file attributes as:
* a file with a name following a template if ``custom_naming`` is ``False`` and ``addhoc_file_path`` is ``None``
* a file within a name set using a file dialog popup if ``custom_naming`` is ``True``
* a file with a custom name if ``addhoc_file_path`` is a ``Path`` object or a path string
Parameters
----------
update_h5: bool
create a new h5 file with name specified by other parameters
if false try to open an existing file and will append new data to it
custom_naming: bool
if True, a selection file dialog opens to set a new file name
addhoc_file_path: Path or str
supplied name by the user for the new file
Returns
-------
update_h5: bool
True if new file has been created, False otherwise
"""
date = datetime.datetime.now()
if addhoc_file_path is None:
if not os.path.isdir(self.settings.child(('base_path')).value()):
os.mkdir(self.settings.child(('base_path')).value())
# set the filename and path
base_name = self.settings.child(('base_name')).value()
if not custom_naming:
custom_naming = self.settings.child(('custom_name')).value()
if not custom_naming:
scan_type = self.settings.child(
('save_type')).value() == 'scan'
scan_path, current_scan_name, save_path = self.update_file_paths(
update_h5)
self.current_scan_name = current_scan_name
self.settings.child(
('current_scan_name')).setValue(current_scan_name)
self.settings.child(
('current_scan_path')).setValue(str(scan_path))
if not scan_type:
self.h5_file_path = save_path #will remove the dataset part used for DAQ_scan datas
self.h5_file_name = base_name + date.strftime(
'_%Y%m%d_%H_%M_%S.h5')
else:
self.h5_file_path = save_path
self.h5_file_name = save_path.name + ".h5"
else:
self.h5_file_name = utils.select_file(start_path=base_name,
save=True,
ext='h5')
self.h5_file_path = self.h5_file_name.parent
else:
if isinstance(addhoc_file_path, str):
addhoc_file_path = Path(addhoc_file_path)
self.h5_file_path = addhoc_file_path.parent
self.h5_file_name = addhoc_file_path.name
fullpathname = str(self.h5_file_path.joinpath(self.h5_file_name))
self.settings.child(('current_h5_file')).setValue(fullpathname)
if update_h5:
self.current_scan_group = None
scan_group = None
if self.current_scan_group is not None:
scan_group = self.current_scan_group._v_name
if update_h5:
self.close_file()
self.h5_file = tables.open_file(fullpathname,
'w',
title='PyMoDAQ file')
self.h5_file.root._v_attrs['pymodaq_version'] = get_version()
else:
self.close_file()
self.h5_file = tables.open_file(fullpathname,
'a',
title='PyMoDAQ file')
self.raw_group = self.get_set_group(self.h5_file.root,
'Raw_datas',
title='Data from PyMoDAQ modules')
self.get_set_logger(self.raw_group)
if scan_group is not None:
self.current_scan_group = self.get_set_group(
self.raw_group, scan_group)
else:
self.current_scan_group = self.get_last_scan()
self.raw_group._v_attrs['type'] = self.settings.child(
('save_type')).value()
self.h5_file.root._v_attrs['file'] = date.strftime(self.h5_file_name)
if update_h5:
self.h5_file.root._v_attrs['date'] = date.strftime('%Y%m%d')
self.h5_file.root._v_attrs['time'] = date.strftime('%H:%M:%S')
return update_h5
def do():
save_file_pathname = select_file(None, save=True,
ext='h5') # see daq_utils
print(save_file_pathname)
def browse_data(fname=None, ret_all=False):
"""
| Browse data present in any h5 file, when user has selected the one,
|
| press OK and returns the selected data
=============== ==================================== ==================================================
**Parameters** **Type** **Description**
*fname* str, Path object The path as a Path object or string
=============== ==================================== ==================================================
=============== ==================================== ==================================================
**Returns** **Type** **Description**
*data* ndarray Data as a numpy array
=============== ==================================== ==================================================
"""
if fname is None:
fname = str(select_file(start_path=None, save=False, ext='h5'))
if type(fname) != str:
try:
fname = str(fname)
except:
raise Exception('filename in browse data is not valid')
if fname != '':
(root, ext) = os.path.splitext(fname)
if not ('h5' in ext or 'hdf5' in ext):
warnings.warn(
'This is not a PyMODAQ h5 file, there could be issues',
Warning)
with tables.open_file(fname) as h5file:
dialog = QtWidgets.QDialog()
dialog.setWindowTitle('Select a data node in the tree')
vlayout = QtWidgets.QVBoxLayout()
form = QtWidgets.QWidget()
browser = H5Browser(form, h5file)
vlayout.addWidget(form)
dialog.setLayout(vlayout)
buttonBox = QtWidgets.QDialogButtonBox(parent=dialog)
dialog.setLayout(vlayout)
buttonBox = QtWidgets.QDialogButtonBox(parent=dialog)
buttonBox.addButton('OK', buttonBox.AcceptRole)
buttonBox.accepted.connect(dialog.accept)
buttonBox.addButton('Cancel', buttonBox.RejectRole)
buttonBox.rejected.connect(dialog.reject)
vlayout.addWidget(buttonBox)
dialog.setWindowTitle('Select data to be loaded')
res = dialog.exec()
if res == dialog.Accepted:
node_path = browser.current_node_path
data = h5file.get_node(
node_path).read() #save preset parameters in a xml file
else:
data = None
node_path = None
if ret_all:
return data, fname, node_path
else:
return data
return None, '', ''
def move_Abs(self, position):
"""
Make the absolute move from the given position after thread command signal was received in DAQ_Move_main.
=============== ========= =======================
**Parameters** **Type** **Description**
*position* float The absolute position
=============== ========= =======================
See Also
--------
DAQ_Move_base.set_position_with_scaling, DAQ_Move_base.poll_moving
"""
try:
position = self.check_bound(position)
#position=self.set_position_with_scaling(position)
#print(position)
self.target_position = position
if self.settings.child(('shaping_type')).value() == 'FullScreen':
self.controller.showBlankscreen(grayValue=position)
elif self.settings.child(
('shaping_type')).value() == 'SplitScreen':
if self.settings.child('splitting', 'split_control').value(
) == 'Screen spliting': #,'GreyA','GreyB']
screenDivider = position
else:
screenDivider = self.settings.child(
'splitting', 'split_value').value()
if self.settings.child('splitting',
'split_control').value() == 'GreyA':
a_gray_value = int(position)
else:
a_gray_value = self.settings.child('splitting',
'greyA_value').value()
if self.settings.child('splitting',
'split_control').value() == 'GreyB':
b_gray_value = int(position)
else:
b_gray_value = self.settings.child('splitting',
'greyB_value').value()
flipped = self.settings.child('splitting',
'split_flip').value()
if self.settings.child('splitting',
'split_dir').value() == 'Vertical':
self.controller.showDividedScreenVertical(
a_gray_value, b_gray_value, screenDivider, flipped)
else:
self.controller.showDividedScreenHorizontal(
a_gray_value, b_gray_value, screenDivider, flipped)
elif self.settings.child(('shaping_type')).value() == 'File':
fname = str(select_file(start_path=None, save=False, ext='h5'))
data = h5browser.browse_data(fname)
if self.settings.child('calibration', 'calib_apply').value(
) and self.calibration is not None:
data = np.reshape(
np.interp(data.reshape(np.prod(data.shape)),
self.calibration,
np.linspace(0, 255, 256)).astype('uint8'),
data.shape)
dataWidth = self.controller.width_px
dataHeight = self.controller.height_px
# Calculate the data:
for indy in range(dataHeight):
for indx in range(dataWidth):
self.data_uchar[indy, indx] = data[indy, indx]
if data is None:
raise Exception('No data has been selected')
else:
self.controller.showData(self.data_uchar)
self.current_position = position #+np.random.rand()-0.5
self.poll_moving()
except Exception as e:
self.emit_status(
ThreadCommand('Update_Status',
[getLineInfo() + str(e), 'log']))
