def test_file_open_close(self, tmp_path, backend):
bck = H5Backend(backend)
title = 'this is a test file'
start_path = get_temp_path(tmp_path, backend)
h5_file = bck.open_file(start_path.joinpath('h5file.h5'), 'w', title)
if backend != 'h5pyd':
assert start_path.joinpath('h5file.h5').exists()
assert start_path.joinpath('h5file.h5').is_file()
assert bck.isopen() is True
assert bck.root().attrs['TITLE'] == title
assert bck.root().attrs['pymodaq_version'] == get_version()
bck.close_file()
assert bck.isopen() is False
#['pyqtgraph.'+x for x in helpers.listAllPackages(pkgroot='examples')])
def get_packages():
packages = find_packages()
for pkg in packages:
if 'hardware.' in pkg:
packages.pop(packages.index(pkg))
return packages
allPackages = get_packages()
setup(
version=get_version(),
#cmdclass={'build': Build,},
# 'install': Install,
# 'deb': helpers.DebCommand,
# 'test': helpers.TestCommand,
# 'debug': helpers.DebugCommand,
# 'mergetest': helpers.MergeTestCommand,
# 'style': helpers.StyleCommand},
packages=allPackages,
#package_dir={'examples': 'examples'}, ## install examples along with the rest of the source
package_data={},
entry_points={
'console_scripts': [
'pymodaq_scan=pymodaq.pymodaq_exec:scan',
'pymodaq_move=pymodaq.pymodaq_exec:move',
'pymodaq_viewer=pymodaq.pymodaq_exec:viewer',
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
copyright = u'%d, Weber Sébastien' % year
author = 'Weber Sebastien'
# 'releases' (changelog) settings
releases_issue_uri = "https://github.com/CEMES-CNRS/PyMoDAQ/issues/%s"
releases_release_uri = "https://github.com/CEMES-CNRS/PyMoDAQ/tree/%s"
sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '..')))
from pymodaq.version import get_version
# Get version info
#
# Branch-only name
version = get_version('branch')
# The full human readable version, including alpha/beta/rc tags.
release = get_version('normal')
# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
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