Table of Contents
- Package PSCalib
- Module PSCalib.CalibFileFinder
- Function PSCalib.CalibFileFinder.deploy_calib_array
- Function PSCalib.CalibFileFinder.deploy_calib_file
- Function PSCalib.CalibFileFinder.find_calib_file
- Function PSCalib.CalibFileFinder.make_calib_file_name
- Function PSCalib.CalibFileFinder.test01
- Function PSCalib.CalibFileFinder.test_deploy_calib_array
- Function PSCalib.CalibFileFinder.test_deploy_calib_file
- Module PSCalib.CalibPars
- Module PSCalib.CalibParsBaseAcqirisV1
- Module PSCalib.CalibParsBaseAndor3dV1
- Module PSCalib.CalibParsBaseAndorV1
- Module PSCalib.CalibParsBaseCameraV1
- Module PSCalib.CalibParsBaseCSPad2x2V1
- Module PSCalib.CalibParsBaseCSPadV1
- Module PSCalib.CalibParsBaseEpix100aV1
- Module PSCalib.CalibParsBaseImpV1
- Module PSCalib.CalibParsBasePnccdV1
- Module PSCalib.CalibParsBasePrincetonV1
- Module PSCalib.CalibParsStore
- Module PSCalib.DCBase
- Module PSCalib.DCConfigParameters
- Module PSCalib.DCDetectorId
- Module PSCalib.DCEmail
- Module PSCalib.DCFileName
- Module PSCalib.DCInterface
- Class PSCalib.DCInterface.DCRangeI
- Class PSCalib.DCInterface.DCStoreI
- Class PSCalib.DCInterface.DCTypeI
- Class PSCalib.DCInterface.DCVersionI
- Function PSCalib.DCInterface.print_warning
- Function PSCalib.DCInterface.test
- Function PSCalib.DCInterface.test_DCRangeI
- Function PSCalib.DCInterface.test_DCStoreI
- Function PSCalib.DCInterface.test_DCTypeI
- Function PSCalib.DCInterface.test_DCVersionI
- Module PSCalib.DCLogger
- Module PSCalib.DCMethods
- Function PSCalib.DCMethods.add_constants
- Function PSCalib.DCMethods.add_constants_to_file
- Function PSCalib.DCMethods.delete_ctype
- Function PSCalib.DCMethods.delete_ctype_from_file
- Function PSCalib.DCMethods.delete_range
- Function PSCalib.DCMethods.delete_range_from_file
- Function PSCalib.DCMethods.delete_version
- Function PSCalib.DCMethods.delete_version_from_file
- Function PSCalib.DCMethods.do_test
- Function PSCalib.DCMethods.evt_to_tsec
- Function PSCalib.DCMethods.get_constants
- Function PSCalib.DCMethods.get_constants_from_file
- Function PSCalib.DCMethods.get_constants_v0
- Function PSCalib.DCMethods.is_good_fname
- Function PSCalib.DCMethods.print_content
- Function PSCalib.DCMethods.print_content_from_file
- Function PSCalib.DCMethods.set_parameters
- Function PSCalib.DCMethods.test_add_constants
- Function PSCalib.DCMethods.test_add_constants_to_file
- Function PSCalib.DCMethods.test_add_constants_two
- Function PSCalib.DCMethods.test_add_text
- Function PSCalib.DCMethods.test_add_text_to_file
- Function PSCalib.DCMethods.test_delete_ctype
- Function PSCalib.DCMethods.test_delete_ctype_from_file
- Function PSCalib.DCMethods.test_delete_range
- Function PSCalib.DCMethods.test_delete_range_from_file
- Function PSCalib.DCMethods.test_delete_version
- Function PSCalib.DCMethods.test_delete_version_from_file
- Function PSCalib.DCMethods.test_get_constants
- Function PSCalib.DCMethods.test_get_constants_from_file
- Function PSCalib.DCMethods.test_misc
- Function PSCalib.DCMethods.test_print_content
- Function PSCalib.DCMethods.test_print_content_from_file
- Module PSCalib.DCRange
- Module PSCalib.DCStore
- Module PSCalib.DCType
- Module PSCalib.DCUtils
- Function PSCalib.DCUtils.create_directory
- Function PSCalib.DCUtils.create_directory_v0
- Function PSCalib.DCUtils.create_path
- Function PSCalib.DCUtils.delete_object
- Function PSCalib.DCUtils.detector_full_name
- Function PSCalib.DCUtils.dettype_from_str_source
- Function PSCalib.DCUtils.do_test
- Function PSCalib.DCUtils.evt_fiducials
- Function PSCalib.DCUtils.evt_time
- Function PSCalib.DCUtils.get_cwd
- Function PSCalib.DCUtils.get_enviroment
- Function PSCalib.DCUtils.get_hostname
- Function PSCalib.DCUtils.get_login
- Function PSCalib.DCUtils.get_subgroup
- Function PSCalib.DCUtils.psana_source
- Function PSCalib.DCUtils.save_object_as_dset
- Function PSCalib.DCUtils.save_string_as_dset
- Function PSCalib.DCUtils.source_full_name
- Function PSCalib.DCUtils.string_from_source
- Function PSCalib.DCUtils.str_tstamp
- Function PSCalib.DCUtils.test_detector_full_name
- Function PSCalib.DCUtils.test_evt_time
- Function PSCalib.DCUtils.test_misc
- Function PSCalib.DCUtils.test_psana_source
- Function PSCalib.DCUtils.test_source_full_name
- Function PSCalib.DCUtils.test_string_from_source
- Module PSCalib.DCVersion
- Module PSCalib.GenericCalibPars
- Module PSCalib.GeometryAccess
- Function PSCalib.GeometryAccess.divide_protected
- Function PSCalib.GeometryAccess.img_default
- Function PSCalib.GeometryAccess.img_from_pixel_arrays
- Function PSCalib.GeometryAccess.test_access
- Function PSCalib.GeometryAccess.test_cspad2x2
- Function PSCalib.GeometryAccess.test_cspad_xy_at_z
- Function PSCalib.GeometryAccess.test_epix100a
- Function PSCalib.GeometryAccess.test_img_default
- Function PSCalib.GeometryAccess.test_load_pars_from_file
- Function PSCalib.GeometryAccess.test_mask_quad
- Function PSCalib.GeometryAccess.test_plot_cspad
- Function PSCalib.GeometryAccess.test_plot_quad
- Function PSCalib.GeometryAccess.test_save_pars_in_file
- Module PSCalib.GeometryObject
- Module PSCalib.GlobalUtils
- Function PSCalib.GlobalUtils.alias_for_src_name
- Function PSCalib.GlobalUtils.calib_dir
- Function PSCalib.GlobalUtils.create_directory
- Function PSCalib.GlobalUtils.det_type_from_source
- Function PSCalib.GlobalUtils.do_test
- Function PSCalib.GlobalUtils.exp_name
- Function PSCalib.GlobalUtils.get_cwd
- Function PSCalib.GlobalUtils.get_enviroment
- Function PSCalib.GlobalUtils.get_hostname
- Function PSCalib.GlobalUtils.get_login
- Function PSCalib.GlobalUtils.load_textfile
- Function PSCalib.GlobalUtils.mask_edges
- Function PSCalib.GlobalUtils.mask_neighbors
- Function PSCalib.GlobalUtils.merge_masks
- Function PSCalib.GlobalUtils.reshape_nda_to_2d
- Function PSCalib.GlobalUtils.reshape_nda_to_3d
- Function PSCalib.GlobalUtils.save_textfile
- Function PSCalib.GlobalUtils.shape_nda_to_2d
- Function PSCalib.GlobalUtils.shape_nda_to_3d
- Function PSCalib.GlobalUtils.string_from_source
- Function PSCalib.GlobalUtils.str_tstamp
- Function PSCalib.GlobalUtils.test_mask_edges_2d
- Function PSCalib.GlobalUtils.test_mask_edges_3d
- Function PSCalib.GlobalUtils.test_mask_neighbors_2d
- Function PSCalib.GlobalUtils.test_mask_neighbors_3d
- Module PSCalib.h5constants
- Module PSCalib.NDArrIO
- Module PSCalib.SegGeometry
- Module PSCalib.SegGeometryCspad2x1V1
- Function PSCalib.SegGeometryCspad2x1V1.test_2x1_img
- Function PSCalib.SegGeometryCspad2x1V1.test_2x1_img_easy
- Function PSCalib.SegGeometryCspad2x1V1.test_2x1_mask
- Function PSCalib.SegGeometryCspad2x1V1.test_pix_sizes
- Function PSCalib.SegGeometryCspad2x1V1.test_xyz_maps
- Function PSCalib.SegGeometryCspad2x1V1.test_xyz_min_max
- Module PSCalib.SegGeometryEpix100V1
- Function PSCalib.SegGeometryEpix100V1.test_2x2_img
- Function PSCalib.SegGeometryEpix100V1.test_2x2_img_easy
- Function PSCalib.SegGeometryEpix100V1.test_2x2_mask
- Function PSCalib.SegGeometryEpix100V1.test_pix_sizes
- Function PSCalib.SegGeometryEpix100V1.test_xyz_maps
- Function PSCalib.SegGeometryEpix100V1.test_xyz_min_max
- Module PSCalib.SegGeometryMatrixV1
- Function PSCalib.SegGeometryMatrixV1.matrix_pars
- Function PSCalib.SegGeometryMatrixV1.test_img
- Function PSCalib.SegGeometryMatrixV1.test_img_easy
- Function PSCalib.SegGeometryMatrixV1.test_mask
- Function PSCalib.SegGeometryMatrixV1.test_pix_sizes
- Function PSCalib.SegGeometryMatrixV1.test_xyz_maps
- Function PSCalib.SegGeometryMatrixV1.test_xyz_min_max
- Module PSCalib.SegGeometryStore
- Module PSCalib.SvnProps
- Module PSCalib.CalibFileFinder
Package PSCalib¶
Module PSCalib.CalibFileFinder¶
PSCalib.CalibFileFinder is a python version of CalibFileFinder.cpp - finds calibration file
Usage:
from PSCalib.CalibFileFinder import CalibFileFinder
cdir = '/reg/d/psdm/CXI/cxi83714/calib/'
group = 'CsPad::CalibV1' # optional parameter, if not available will be set for src from dict
src = 'CxiDs1.0:Cspad.0'
type = 'pedestals'
rnum = 137
cff = CalibFileFinder(cdir, group, pbits=0377)
#OR
cff = CalibFileFinder(cdir)
fname = cff.findCalibFile(src, type, rnum)
fname_new = cff.makeCalibFileName(src, type, run_start, run_end=None)
#-----------------------------------------------
# ALTERNATIVE usage of direct access methods
from PSCalib.CalibFileFinder import find_calib_file, make_calib_file_name
fname_existing = find_calib_file(cdir, src, type, rnum, pbits=1)
fname_new = make_calib_file_name(cdir, src, type, run_start, run_end=None, pbits=1)
#-----------------------------------------------
# Deploy file or numpy array as a file in the calibration store
# use optional dictionary of comments to save in the HISTORY and file
arr = np.ones((32,185,388))
cmts = {'exp':'cxi12345', 'ifname':'input-file-name', 'app':'my-app-name', 'comment':'my-comment'}
deploy_calib_array(cdir, src, type, run_start, run_end, arr, cmts, fmt='%.1f', pbits=1)
cmts = {'exp':'cxi12345', 'app':'my-app-name', 'comment':'my-comment'}
ifname='path-to-my-own-calibtation-file/file-name.txt'
deploy_calib_file(cdir, src, type, run_start, run_end, ifnameq, cmts, pbits=1)
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 12322 $
Version: $Id: CalibFileFinder.py 8469 2014-06-24 22:55:21Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Function PSCalib.CalibFileFinder.deploy_calib_array¶
-
PSCalib.CalibFileFinder.deploy_calib_array(cdir, src, type, run_start, run_end=None, arr=None, dcmts={}, fmt='%.1f', pbits=1)[source]¶ Deploys array in calibration file
- makes the new file name using make_calib_file_name(...)
- if file with this name already exists - rename it with current timestamp in the name
- save array in file
- add history record
Function PSCalib.CalibFileFinder.deploy_calib_file¶
-
PSCalib.CalibFileFinder.deploy_calib_file(cdir, src, type, run_start, run_end=None, ifname='', dcmts={}, pbits=1)[source]¶ Deploys calibration file
- makes the new file name using make_calib_file_name(...)
- if file with this name already exists - rename it with current timestamp in the name
- save array in file
- add history record
Module PSCalib.CalibPars¶
CalibPars - abstract interface for access to calibration parameters.
Methods of this class should be re-implemented in derived classes with name pattern CalibPars<Detector>
for different type of detectore. For example, CSPAD can be implemented in class PSCalib.CalibParsCspadV1
which enherits from PSCalib.CalibPars, etc.
Currently implementation of this interface for all detectors is done in class PSCalib.GenericCalibPars.
Access to all detectors is available through the factory method in class PSCalib.CalibParsStore.
Usage of (implemented) interface methods:
from PSCalib.CalibPars import CalibPars
import PSCalib.GlobalUtils as gu
cp = CalibPars()
cp.print_attrs()
size = cp.pedestals()
size = cp.pixel_status()
size = cp.pixel_rms()
size = cp.pixel_gain()
size = cp.pixel_mask()
size = cp.pixel_bkgd()
size = cp.common_mode()
ctype = gu.PEDESTALS # ex.: gu.PIXEL_STATUS, gu.PIXEL_RMS, gu.PIXEL_MASK, etc.
size = cp.ndim(ctype)
size = cp.size(ctype)
size = cp.shape(ctype)
size = cp.status(ctype)
See also: GenericCalibPars, PSCalib.CalibParsStore
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10647 $
Version: $Id: CalibPars.py 10647 2015-09-09 15:20:25Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseAcqirisV1¶
CalibParsBaseAcqirisV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10630 $
Version: $Id: CalibParsBaseAcqirisV1.py 10630 2015-08-27 23:07:27Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseAndor3dV1¶
CalibParsBaseAndor3dV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 11400 $
Version: $Id: CalibParsBaseAndor3dV1.py 11400 2016-02-23 00:07:50Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseAndorV1¶
CalibParsBaseAndorV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10630 $
Version: $Id: CalibParsBaseAndorV1.py 10630 2015-08-27 23:07:27Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseCameraV1¶
CalibParsBaseCameraV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10630 $
Version: $Id: CalibParsBaseCameraV1.py 10630 2015-08-27 23:07:27Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseCSPad2x2V1¶
CalibParsBaseCSPad2x2V1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10630 $
Version: $Id: CalibParsBaseCSPad2x2V1.py 10630 2015-08-27 23:07:27Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseCSPadV1¶
CalibParsBaseCSPadV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10630 $
Version: $Id: CalibParsBaseCSPadV1.py 10630 2015-08-27 23:07:27Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseEpix100aV1¶
CalibParsBaseEpix100aV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 12703 $
Version: $Id: CalibParsBaseEpix100aV1.py 12703 2016-10-03 21:13:53Z cpo@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBaseImpV1¶
CalibParsBaseImpV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10699 $
Version: $Id: CalibParsBaseImpV1.py 10699 2015-09-18 18:52:52Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBasePnccdV1¶
CalibParsBasePnccdV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10647 $
Version: $Id: CalibParsBasePnccdV1.py 10647 2015-09-09 15:20:25Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsBasePrincetonV1¶
CalibParsBasePrincetonV1 - holds basic calibration metadata parameters for associated detector.
See also: PSCalib.CalibPars, PSCalib.CalibParsStore.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10630 $
Version: $Id: CalibParsBasePrincetonV1.py 10630 2015-08-27 23:07:27Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.CalibParsStore¶
PSCalib.CalibParsStore - is a factory class/method to switch between different device-dependent
segments/sensors to access their pixel geometry uling PSCalib.SegGeometry interface.
Usage:
# Import
from PSCalib.CalibParsStore import cps
from PSCalib.GlobalUtils import *
# Initialization
calibdir = env.calibDir() # or e.g. '/reg/d/psdm/<INS>/<experiment>/calib'
group = None # or e.g. 'CsPad::CalibV1'
source = 'Camp.0:pnCCD.1'
runnum = 10 # or e.g. evt.run()
pbits = 255
o = cps.Create(calibdir, group, source, runnum, pbits)
# or using different list of parameters to access calibration from hdf5 DCS file:
o = cps.CreateForEvtEnv(self, calibdir, group, source, evt, env, pbits=0)
# Access methods
nda = o.pedestals()
nda = o.pixel_status()
nda = o.pixel_rms()
nda = o.pixel_mask()
nda = o.pixel_gain()
nda = o.pixel_bkgd()
nda = o.common_mode()
status = o.status(ctype=PEDESTALS) # see list of ctypes in :py:class:`PSCalib.GlobalUtils`
shape = o.shape(ctype)
size = o.size(ctype)
ndim = o.ndim(ctype)
- @see
PSCalib.GenericCalibParsPSCalib.GlobalUtilsPSCalib.CalibParsPSCalib.CalibParsStorePSCalib.CalibParsBaseAndorV1PSCalib.CalibParsBaseAndor3dV1PSCalib.CalibParsBaseCameraV1PSCalib.CalibParsBaseCSPad2x2V1PSCalib.CalibParsBaseCSPadV1PSCalib.CalibParsBaseEpix100aV1PSCalib.CalibParsBasePnccdV1PSCalib.CalibParsBasePrincetonV1PSCalib.CalibParsBaseAcqirisV1PSCalib.CalibParsBaseImpV1
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Module PSCalib.DCBase¶
PSCalib.DCBase - base class for the Detector Calibration (DC) project.
Usage:
# Import
from PSCalib.DCBase import DCBase
o = DCBase()
# Dictionary of parameters
# ========================
o.set_pars_dict(d) # set (dict) dictionary of pars.
o.add_par(k,v) # add (k,v) par to the dictionary of pars.
o.del_par(k) # delete par with key k.
o.clear_pars() # delete all pars from the dictionary.
d = o.pars_dict() # returns (dict) dictionary of pars.
p = o.par(k) # returns par value for key k.
t = o.pars_text() # returns (str) text of all pars.
# History records
# ===============
o.set_history_dict(d) # set (dict) dictionary of history from specified dictionary
o.add_history_record(rec, tsec=None) # add (str) record with (int) time[sec] to the history dictionary of (tsec:rec).
# If tsec is None - current time is used as a key.
o.del_history_record(tsec) # Delete one history record from the dictionary by its time tsec.
o.clear_history() # Delete all history records from the dictionary.
d = o.history_dict() # returns (dict) history dictionary associated with current object .
r = o.history_record(tsec) # returns (str) history record for specified time tsec.
t = o.history_text(tsfmt=None) # returns (str) all history records preceded by the time stamp as a text.
# Save and Load
# =============
o.save_history_file(path='history.txt', verb=False) # save history in the text file
o.load_history_file(path='history.txt', verb=False) # load history from the text file
o.save_base(grp) # save everything in hdf5 group
o.load_base(name, grp) # load from hdf5 group
# Time convertors
# ===============
t_str = o.tsec_to_tstr(tsec, tsfmt=None) # converts (float) time[sec] to the (str) time stamp
t_sec = o.tstr_to_tsec(tstr, tsfmt=None) # converts (str) time stamp to (float) time[sec]
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCBase.py 12879 2016-11-17 22:15:26Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Class PSCalib.DCBase.DCBase¶
-
class
PSCalib.DCBase.DCBase(cmt=None)[source]¶ Base class for the Detector Calibration (DC) project.
Parameters
cmt : str - string of comment associated with derived class object.
-
history_text(tsfmt=None)[source]¶ Returns (str) history records preceded by the time stamp as a text
-
make_record(action='', key='', cmt=False)[source]¶ Returns string record combined with comment.
Parameters
action : str - description of method action, key : str - key for hdf5 group or dataset name, cmt : str/None/False - additional comment or no-comment: False is used to turn off history record, None - no-comment.
-
tsec_to_tstr(tsec, tsfmt=None, addfsec=True)[source]¶ converts float tsec like 1471035078.908067 to the string 2016-08-12T13:51:18.908067
-
tstr_to_tsec(tstr, tsfmt=None)[source]¶ converts string tstr like 2016-08-12T13:51:18.908067 to the float time in seconds 1471035078.908067
-
_offspace= ' '¶
-
_tsfmt= '%Y-%m-%dT%H:%M:%S'¶
-
Module PSCalib.DCConfigParameters¶
DCConfigParameters - class supporting configuration parameters for application.
See also: base class CalibManager.ConfigParameters
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id:DCConfigParameters.py 11923 2016-05-17 21:14:33Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.DCDetectorId¶
PSCalib.DCDetectorId - class for the Detector Calibration (DC) project.
Usage:
# Import
from PSCalib.DCDetectorId import id_epix, id_cspad
# Parameters
dsn = 'exp=cxif5315:run=169'
# or
dsn = '/reg/g/psdm/detector/data_test/types/0003-CxiDs2.0-Cspad.0-fiber-data.xtc'
ds = psana.DataSource(dsn)
env = ds.env()
src = psana.Source('CxiDs2.0:Cspad.0') # or unique portion of the name ':Cspad.' or alias 'DsaCsPad'
# Access methods
ide = id_epix(env, src)
idc = id_cspad(env, src)
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCDetectorId.py 12871 2016-11-14 22:19:31Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.DCEmail¶
PSCalib.DCEmail - class for Detector Calibration Store (DCS) project.
Usage:
# Import
from PSCalib.DCEmail import send_text_email
# Send message via e-mail
send_text_email(msg='Text message', subject='Text subject', email_from='do-not-reply@slac.stanford.edu', email_to='do-not-send@slac.stanford.edu')
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCEmail.py 12660 2016-09-27 00:33:40Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.DCFileName¶
PSCalib.DCFileName - file name object for Detector Calibration Store (DCS) project.
Usage:
# Import
from PSCalib.DCFileName import DCFileName
# Instatiation
o = DCFileName(env, 'Epix', calibdir='path-to/calib')
# Methods
o.set_dettype(env, src)
o.set_detid(env, src)
status = o.make_path_to_calib_file(mode=0770)
dt = o.dettype()
did = o.detid()
dn = o.detname()
fname = o.calib_file_name() # e.g., epix100a-3925868555.h5
fdir = o.calib_file_dir() # e.g., /reg/neh/home4/dubrovin/LCLS/rel-calib/calib
fpath = o.calib_file_path() # e.g., /reg/neh/home4/dubrovin/LCLS/rel-calib/calib/epix100a/epix100a-3925868555.h5
fdir = o.calib_file_dir_repo() # e.g., /reg/g/psdm/detector/calib/epix100a/
fpath = o.calib_file_path_repo() # e.g., /reg/g/psdm/detector/calib/epix100a/epix100a-3925868555.h5
o.print_attrs() # print attributes
o.log_attrs() # dump attributes in the logger
s = o.str_attrs() # returns a string of attributes
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCFileName.py 12777 2016-10-19 21:37:38Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.DCInterface¶
PSCalib.DCInterface - abstract interface for the Detector Calibration (DC) project.
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCInterface.py 12730 2016-10-11 21:11:56Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Class PSCalib.DCInterface.DCRangeI¶
-
class
PSCalib.DCInterface.DCRangeI(begin, end, cmt=None)[source]¶ Abstract interface class for the Detector Calibration (DC) project
o = DCRangeI(begin, end)
tsbegin = o.begin() # (int) time stamp beginning validity range tsend = o.end() # (int) time stamp ending validity range dico = o.versions() # (list of uint) versions of calibrations vnum = o.vnum_def() # (DCVersion ~ h5py.Group) reference to the default version in the time-range object vo = o.version(vers) # (DCVersion ~ h5py.Group) specified version in the time-range object bool = o.tsec_in_range(tsec) # (bool) True/False if tsec is/not in the validity range bool = o.evt_in_range(evt) # (bool) True/False if evt is/not in the validity range o.set_begin(tsbegin) # set (int) time stamp beginning validity range o.set_end(tsend) # set (int) time stamp ending validity range o.add_version(vers) # set (DCVersion ~ h5py.Group) versions of calibrations o.set_versdef(vers) # set (DCVersion ~ h5py.Group) versions of calibrations vnum = o.mark_version(vers) # del version o.mark_versions() # del all registered versions
Class PSCalib.DCInterface.DCStoreI¶
-
class
PSCalib.DCInterface.DCStoreI(fname, cmt=None)[source]¶ Abstract interface class for the Detector Calibration (DC) project
cs = DCStoreI(fname)
tscfile = cs.tscfile() # (int) time stamp of the file creation dettype = cs.dettype() # (str) detector type detid = cs.detid() # (str) detector id detname = cs.detname() # (str) detector name of self object predecessor = cs.predecessor() # (str) detname of predecessor or None successor = cs.successor() # (str) detname of successor or None ctypes = cs.ctypes() # (list) calibration types in the file cto = cs.ctypeobj(ctype) # (DCType ~ h5py.Group) calibration type object
cs.set_tscfile(ts) # set (int) time stamp of the file creation cs.set_dettype(dettype) # set (str) detector type cs.set_detid(detid) # set (str) detector id cs.set_detname(detname) # set (str) detector name of self object cs.set_predecessor(pred) # set (str) detname of predecessor or None cs.set_successor(succ) # set (str) detname of successor or None cs.add_ctype(ctype) # add (str) calibration type to the DCStore object ct = cs.mark_ctype(ctype) # mark ctype (str) from the DCStore object, returns (str) ctype or None cs.mark_ctypes() # mark all ctypes from the DCStore object cs.clear_ctypes(ctype) # clear dictionary of ctypes in the DCStore object cs.save(path, mode) # save current calibration in the file specified by path, if path is Null - update current file. cs.load(path) # load content of the file in DCStore object
Class PSCalib.DCInterface.DCTypeI¶
-
class
PSCalib.DCInterface.DCTypeI(ctype, cmt=None)[source]¶ Abstract interface class for the Detector Calibration (DC) project
cto = DCTypeI(type)
ctype = cto.ctype() # (str) of ctype name ranges = cto.ranges() # (list) of time ranges for ctype ro = cto.rangeobj(begin, end) # (DCRange ~ h5py.Group) time stamp validity range object ro = cto.range_for_tsec(tsec) # (DCRange) range object for time stamp in (double) sec ro = cto.range_for_evt(evt) # (DCRange) range object for psana.Evt object cto.add_range(tsr) # add (str) of time ranges for ctype keyr = cto.mark_range(begin, end) # mark range from the DCType object keyr = cto.mark_range_for_key(keyr) # mark range from the DCType object cto.mark_ranges(tsr) # mark all ranges from the DCType object cto.print_obj()
Class PSCalib.DCInterface.DCVersionI¶
-
class
PSCalib.DCInterface.DCVersionI(vnum, tsprod=None, arr=None, cmt=None)[source]¶ Abstract interface class for the Detector Calibration (DC) project
o = DCVersionI(vnum, tsprod=None, arr=None)
o.set_vnum(vnum) # sets (int) version o.set_tsprod(tsprod) # sets (double) time stamp of the version production o.add_data(nda) # sets (np.array) calibration array vnum = o.vnum() # returns (int) version number s_vnum = o.str_vnum() # returns (str) version number tsvers = o.tsprod() # returns (double) time stamp of the version production nda = o.data() # returns (np.array) calibration array o.save(group) # saves object content under h5py.group in the hdf5 file. o.load(group) # loads object content from the h5py.group of hdf5 file.
Module PSCalib.DCLogger¶
DCLogger - logger for Detector Calibration Store.
See also: base class CalibManager.Logger
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id:DCLogger.py 11923 2016-05-17 21:14:33Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.DCMethods¶
PSCalib.DCMethods - contains a set of utilities for direct operations with calibration data.
Usage:
# Import
import PSCalib.DCMethods as dcm
# Example of parameters
dsname = 'exp=cxif5315:run=129'
# or:
dsname = '/reg/g/psdm/detector/data_test/xtc/cxif5315-e545-r0169-s00-c00.xtc'
src = 'Cspad.' # 'Epix100a.', etc
ctype = gu.PIXEL_MASK # OR: gu.PEDESTALS, gu.PIXEL_STATUS, etc.
vers = None # or e.g. 5
calibdir = None # or e.g. './calib'
nda = np.zeros((32,185,388))
pred = 'CxiDs2.0:Cspad.0'
succ = 'CxiDs2.0:Cspad.0'
range = '1474587520-end'
# Methods with dynamically-reconstruction of calib file name
dcm.add_constants(nda, evt, env, src, ctype, calibdir, vers=None, pred=None, succ=None, cmt=None)
dcm.print_content(env, src, calibdir=None)
nda = dcm.get_constants(evt, env, src, ctype, calibdir=None, vers=None, verb=False)
dcm.delete_version(evt, env, src, ctype, calibdir=None, vers=None, verb=False)
dcm.delete_range (evt, env, src, ctype, calibdir, range, cmt, verb)
dcm.delete_ctype (evt, env, src, ctype, calibdir, cmt, verb)
# Methods using fname
dcm.add_constants_to_file(data, fname, par, env, ctype, vers=None, pred=None, succ=None, cmt=None)
dcm.print_content_from_file(fname)
nda = dcm.get_constants_from_file(fname, evt, ctype, vers=None, verb=False)
dcm.delete_version_from_file(fname, ctype, vers=None, cmt=None, verb=False)
dcm.delete_range_from_file (fname, ctype, range, cmt, verb)
dcm.delete_ctype_from_file (fname, ctype, cmt, verb)
- See also: methods
add_constants(),add_constants_to_file(),print_content(),print_content_from_file(),get_constants(),get_constants_from_file(),delete_version(),delete_version_from_file(),delete_range(),delete_range_from_file(),delete_ctype()delete_ctype_from_file()- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: 2016-09-23$
Author: Mikhail S. Dubrovin
Function PSCalib.DCMethods.add_constants¶
-
PSCalib.DCMethods.add_constants(data, evt, env, src='Epix100a.', ctype=4, calibdir=None, vers=None, pred=None, succ=None, cmt=None, verb=False)[source]¶ Adds specified numpy array to the hdf5 file.
Parameters
data : numpy.array or str - array or string of calibration constants/data to save in file env : psana.Env -> full detector name for psana.Source evt : psana.Event -> event time src : str - source short/full name, alias or full ctype: gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK calibdir : str - fallback path to calib dir (if xtc file is copied - calib and experiment name are lost) vers : int - calibration version pred : str - predecessor name succ : str - successor name cmt : str - comment saved as a history record within DCRange verb : bool - verbosity, default=False - do not prnt any message
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.add_constants_to_file¶
-
PSCalib.DCMethods.add_constants_to_file(data, fname, par, env=None, ctype=4, vers=None, pred=None, succ=None, cmt=None, verb=False)[source]¶ Adds specified numpy array to the hdf5 file.
Parameters
data : numpy.array or str - array or string of calibration constants/data to save in file fname: full path to the hdf5 file par : psana.Event | float - tsec event time env : psana.Env -> full detector name for psana.Source ctype: gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK vers : int - calibration version pred : str - predecessor name succ : str - successor name cmt : str - comment saved as a history record within DCRange verb : bool - verbosity, default=False - do not prnt any message
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.delete_ctype¶
-
PSCalib.DCMethods.delete_ctype(evt, env, src='Epix100a.', ctype=4, calibdir=None, cmt=None, verb=False)[source]¶ Delete specified ctype from calibration constants.
Parameters
evt : psana.Event -> event time env : psana.Env -> full detector name for psana.Source src : str - source short/full name, alias or full ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK calibdir : str - fallback path to calib dir (if xtc file is copied - calib and experiment name are lost) cmt : str - comment verb : bool - verbousity
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.delete_ctype_from_file¶
-
PSCalib.DCMethods.delete_ctype_from_file(fname, ctype=4, cmt=None, verb=False)[source]¶ Delete specified ctype from calibration constants.
Parameters
fname : full path to the hdf5 file ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK cmt : str - comment verb : bool - verbousity
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.delete_range¶
-
PSCalib.DCMethods.delete_range(evt, env, src='Epix100a.', ctype=4, calibdir=None, range=None, cmt=None, verb=False)[source]¶ Delete specified time range from calibration constants.
Parameters
evt : psana.Event -> event time env : psana.Env -> full detector name for psana.Source src : str - source short/full name, alias or full ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK calibdir : str - fallback path to calib dir (if xtc file is copied - calib and experiment name are lost) range : str - range, e.g. ‘1474587520-end’ cmt : str - comment verb : bool - verbousity
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.delete_range_from_file¶
-
PSCalib.DCMethods.delete_range_from_file(fname, ctype=4, range=None, cmt=None, verb=False)[source]¶ Delete specified time range from calibration constants.
Parameters
fname : full path to the hdf5 file ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK range : str - range, e.g. ‘1474587520-end’ cmt : str - comment verb : bool - verbousity
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.delete_version¶
-
PSCalib.DCMethods.delete_version(evt, env, src='Epix100a.', ctype=4, calibdir=None, vers=None, cmt=None, verb=False)[source]¶ Delete specified version from calibration constants.
Parameters
evt : psana.Event -> event time env : psana.Env -> full detector name for psana.Source src : str - source short/full name, alias or full ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK calibdir : str - fallback path to calib dir (if xtc file is copied - calib and experiment name are lost) vers : int - calibration version cmt : str - comment verb : bool - verbousity
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.delete_version_from_file¶
-
PSCalib.DCMethods.delete_version_from_file(fname, par, ctype=4, vers=None, cmt=None, verb=False)[source]¶ Delete specified version from calibration constants.
Parameters
fname : full path to the hdf5 file par : psana.Event | float - tsec event time ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK vers : int - calibration version cmt : str - comment verb : bool - verbousity
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.get_constants¶
-
PSCalib.DCMethods.get_constants(par, env, src='Epix100a.', ctype=4, calibdir=None, vers=None, verb=False)[source]¶ Returns specified array of calibration constants.
Parameters
par : psana.Event | float - tsec event time env : psana.Env -> full detector name for psana.Source src : str - source short/full name, alias or full ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK calibdir : str - fallback path to calib dir (if xtc file is copied - calib and experiment name are lost) vers : int - calibration version
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.get_constants_from_file¶
-
PSCalib.DCMethods.get_constants_from_file(fname, par, ctype=4, vers=None, verb=False)[source]¶ Returns specified array of calibration constants.
Parameters
fname : full path to the hdf5 file par : psana.Event | float - tsec event time ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK vers : int - calibration version
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.print_content¶
-
PSCalib.DCMethods.print_content(env, src='Epix100a.', calibdir=None)[source]¶ Defines the file name and prints file content.
Parameters
env : psana.Env -> full detector name for psana.Source src : str - source short/full name, alias or full calibdir : str - fallback path to calib dir (if xtc file is copied - calib and experiment name are lost)
Back to
PSCalib.DCMethods
Function PSCalib.DCMethods.print_content_from_file¶
-
PSCalib.DCMethods.print_content_from_file(fname)[source]¶ Prints content of the file.
Parameters
fname : str - full path to the file
Back to
PSCalib.DCMethods
Module PSCalib.DCRange¶
PSCalib.DCRange - class for the Detector Calibration (DC) project.
Usage:
# Import
from PSCalib.DCRange import DCRange
# Initialization
o = DCRange(begin, end=None, cmt=None)
# Methods
str_range = o.range() # (str) of the time stamp validity range
t_sec = o.begin() # (double) time stamp beginning validity range
t_sec = o.end() # (double) time stamp ending validity range or (str) 'end'
dico = o.versions() # (list of uint) versions of calibrations
v = o.vnum_def() # returns default version number
v = o.vnum_last() # returns last version number
vo = o.version(vnum=None) # returns version object for specified version
ts_in_range = o.tsec_in_range(tsec) # (bool) True/False if tsec is/not in the validity range
evt_in_range= o.evt_in_range(evt) # (bool) True/False if evt is/not in the validity range
o.set_begin(tsbegin) # set (int) time stamp beginning validity range
o.set_end(tsend) # set (int) time stamp ending validity range
o.add_version(vnum=None, tsec_prod=None, nda=None, cmt=None) # add object for new version of calibration data
o.set_vnum_def(vnum=None) # set default version number, if available. vnum=None - use last available.
vd = o.mark_version(vnum=None) # mark version for deletion, returns version number or None if nothing was deleted
o.mark_versions() # mark all registered versions for deletion
o.save(group) # saves object content under h5py.group in the hdf5 file.
o.load(group) # loads object content from the hdf5 file.
o.print_obj() # print info about this object and its children
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCRange.py 12730 2016-10-11 21:11:56Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Class PSCalib.DCRange.DCRange¶
Module PSCalib.DCStore¶
PSCalib.DCStore class for the Detector Calibration (DC) project.
Usage:
# Import
from PSCalib.DCStore import DCStore
# Initialization
o = DCStore(fpath)
# Methods
tscfile = o.tscfile() # (double) time stamp of the file creation
dettype = o.dettype() # (str) detector type
detid = o.detid() # (str) detector id
detname = o.detname() # (str) detector name of self object
predecessor = o.predecessor() # (str) detname of predecessor or None
successor = o.successor() # (str) detname of successor or None
ctypes = o.ctypes() # (list) calibration types in the file
cto = o.ctypeobj(ctype) # (DCType ~ h5py.Group) calibration type object
o.set_tscfile(tsec) # set (double) time stamp of the file creation
o.set_dettype(dettype) # set (str) detector type
o.set_detid(detid) # set (str) detector id
o.set_detname(detname) # set (str) detector name of self object
o.set_predecessor(pred) # set (str) detname of predecessor or None
o.set_successor(succ) # set (str) detname of successor or None
o.add_ctype(ctype) # add (str) calibration type to the DCStore object
ctype = o.mark_ctype(ctype) # delete ctype (str) from the DCStore object, returns ctype or None
o.mark_ctypes() # delete all ctypes (str) from the DCStore object
o.clear_ctype() # clear all ctypes (str) from the DCStore object dictionary
o.save(group, mode='r+') # saves object in hdf5 file. mode='r+'/'w' update/rewrite file.
o.load(group) # loads object content from the hdf5 file.
o.print_obj() # print info about this object and its children
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCStore.py 12730 2016-10-11 21:11:56Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Class PSCalib.DCStore.DCStore¶
Module PSCalib.DCType¶
PSCalib.DCType - class for the Detector Calibration (DC) project.
Usage:
# Import
from PSCalib.DCType import DCType
# Initialization
o = DCType(type)
# Methods
o.set_ctype(ctype) # add (str) of time ranges for ctype.
ctype = o.ctype() # returns (str) of ctype name.
ranges = o.ranges() # returns (dict) of time range objects.
range = o.range(begin, end) # returns time stamp validity range object.
ro = o.range_for_tsec(tsec) # (DCRange) range object for time stamp in (double) sec
ro = o.range_for_evt(evt) # (DCRange) range object for psana.Evt object
o.add_range(begin, end) # add (str) of time ranges for ctype.
kr = o.mark_range(begin, end) # mark range from the DCType object, returns (str) key or None
kr = o.mark_range_for_key(keyrange)# mark range specified by (str) keyrange from the DCType object, returns (str) key or None
o.mark_ranges() # mark all ranges from the DCType object
o.clear_ranges() # delete all range objects from dictionary.
o.save(group) # saves object content under h5py.group in the hdf5 file.
o.load(group) # loads object content from the hdf5 file.
o.print_obj() # print info about this object and its children
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCType.py 12730 2016-10-11 21:11:56Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Class PSCalib.DCType.DCType¶
-
class
PSCalib.DCType.DCType(ctype, cmt=None)[source]¶ Class for the Detector Calibration (DC) project
Parameters
ctype : gu.CTYPE - enumerated calibration type cmt : str - comment
-
range_for_evt(evt)[source]¶ Return DCRange object from all available which range validity is matched to the evt time.
-
Module PSCalib.DCUtils¶
PSCalib.DCUtils - contains a set of utilities
Usage:
# Import
import PSCalib.DCUtils as gu
# Methods
# Get string with time stamp, ex: 2016-01-26T10:40:53
ts = gu.str_tstamp(fmt='%Y-%m-%dT%H:%M:%S', time_sec=None)
usr = gu.get_enviroment(env='USER')
usr = gu.get_login()
host = gu.get_hostname()
cwd = gu.get_cwd()
gu.create_directory(dir, mode=0775)
gu.create_path(path, depth=2, mode=0775)
gu.save_string_as_dset(grp, name, s)
src = gu.source_full_name(env, src)
dtype = gu.dettype_from_str_source(src)
src = gu.string_from_source(source) # source is psana.Source object or string like
# 'CxiDs2.0:Cspad.0' from 'DetInfo(CxiDs2.0:Cspad.0)'
dname = gu.detector_full_name(env, src)
source = gu.psana_source(env, srcpar)
t_sec = gu.evt_time(evt)
fid = gu.evt_fiducials(evt)
# methods for HDF5
sg = gu.get_subgroup(grp, subgr_name)
gu.delete_object(grp, oname)
gu.save_object_as_dset(grp, name, shape=None, dtype=None, data=0)
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Function PSCalib.DCUtils.psana_source¶
-
PSCalib.DCUtils.psana_source(env, srcpar)[source]¶ returns psana.Source(src) from other psana.Source brief src or alias.
Parameters
srcpar : str - regular source or its alias, ex.: ‘XppEndstation.0:Rayonix.0’ or ‘rayonix’ set_sub : bool - default=True - propagates source parameter to low level package
Module PSCalib.DCVersion¶
PSCalib.DCVersion - class for the Detector Calibration (DC) project.
Usage:
# Import
from PSCalib.DCVersion import DCVersion
# Initialization
o = DCVersion(vnum, tsprod=None, arr=None, cmt=None)
# Methods
o.set_vnum(vnum) # sets (int) version
o.set_tsprod(tsprod) # sets (double) time stamp of the version production
o.add_data(data) # sets (str or np.array) calibration data
vnum = o.vnum() # returns (int) version number
s_vnum = o.str_vnum() # returns (str) version number
tsvers = o.tsprod() # returns (double) time stamp of the version production
data = o.data() # returns (np.array) calibration array
o.save(group) # saves object content under h5py.group in the hdf5 file.
o.load(group) # loads object content from the h5py.group of hdf5 file.
o.print_obj() # print info about this object.
# and all methods inherited from PSCalib.DCBase
- See also: project modules
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: DCVersion.py 12898 2016-11-22 19:27:56Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Class PSCalib.DCVersion.DCVersion¶
Module PSCalib.GenericCalibPars¶
GenericCalibPars - implementation of CalibPars interface methods for generic detectors.
Usage:
# THIS CLASS IS NOT SUPPOSED TO BE USED AS SELF-DEPENDENT...
# USE :py:class:`PSCalib.CalibParsStore`
from PSCalib.GenericCalibPars import GenericCalibPars
from PSCalib.CalibParsBaseAndorV1 import CalibParsBaseAndorV1
from PSCalib.CalibParsBaseCameraV1 import CalibParsBaseCameraV1
from PSCalib.CalibParsBaseCSPad2x2V1 import CalibParsBaseCSPad2x2V1
...
from PSCalib.CalibParsBasePnccdV1 import CalibParsBasePnccdV1
cbase = CalibParsBasePnccdV1()
calibdir = '/reg/d/psdm/CXI/cxif5315/calib'
group = 'PNCCD::CalibV1'
source = 'CxiDs2.0:Cspad.0'
runnum = 60
pbits = 255
ctype = gu.PEDESTALS
gcp = GenericCalibPars(cbase, calibdir, group, source, runnum, pbits)
nda = gcp.pedestals()
nda = gcp.pixel_rms()
nda = gcp.pixel_mask()
nda = gcp.pixel_bkgd()
nda = gcp.pixel_status()
nda = gcp.pixel_gain()
nda = gcp.common_mode()
status = gcp.get_status(ctype=PEDESTALS) # see list of ctypes in :py:class:`PSCalib.GlobalUtils`
shape = gcp.get_shape(ctype)
size = gcp.get_size(ctype)
ndim = gcp.get_ndim(ctype)
nda = gcp.set_version(vers=None)
nda = gcp.constants_default(ctype)
nda = gcp.constants_calib(ctype)
nda = gcp.constants_dcs(ctype, vers=None, verb=False)
nda = gcp.constants(ctype, vers=None, verb=False)
See also: PSCalib.CalibPars, PSCalib.CalibParsStore, PSCalib.CalibParsCspad2x1V1, :py:class:`PSCalib.GlobalUtils
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 12953 $
Version: $Id: GenericCalibPars.py 12953 2016-12-08 17:21:15Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.GeometryAccess¶
GeometryAccess - holds and access hierarchical geometry for generic pixel detector
Usage:
from PSCalib.GeometryAccess import GeometryAccess, img_from_pixel_arrays
fname_geometry = '/reg/d/psdm/CXI/cxitut13/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/geometry/0-end.data'
geometry = GeometryAccess(fname_geometry, 0377)
# load constants from geometry file
geometry.load_pars_from_file(path=None)
# load constants from '
- ‘-separated str / text object
geometry.load_pars_from_str(s)
# check if geometry info is available, returns bool status = geometry.is_valid()
# get pixel coordinate [um] arrays X, Y, Z = geometry.get_pixel_coords(oname=None, oindex=0, do_tilt=True)
# get pixel x,y coordinate [um] arrays projected toward origin on specified zplane, if zplane=None then zplane=Z.mean() X, Y = geometry.get_pixel_xy_at_z(zplane=None, oname=None, oindex=0, do_tilt=True)
# print a portion of pixel X, Y, and Z coordinate arrays geometry.print_pixel_coords(oname=None, oindex=0)
# get pixel area array; A=1 for regular pixels, =2.5 for wide. area = geometry.get_pixel_areas(oname=None, oindex=0)
# returns (smallest) pixel size [um] pixel_size = geometry.get_pixel_scale_size(oname=None, oindex=0)
# returns dictionary of comments associated with geometry (file) dict_of_comments = geometry.get_dict_of_comments()
# print comments associated with geometry (file) geometry.print_comments_from_dict()
# print list of geometry objects geometry.print_list_of_geos()
# print list of geometry object children geometry.print_list_of_geos_children()
# get pixel mask array; # mbits = +1-mask edges, +2-wide pixels, +4-non-bonded pixels, +8/+16 - four/eight neighbours of non-bonded mask = geometry.get_pixel_mask(oname=None, oindex=0, mbits=0377)
# get index arrays for entire detector iX, iY = geometry.get_pixel_coord_indexes(do_tilt=True)
# get index arrays for specified quad with offset iX, iY = geometry.get_pixel_coord_indexes(‘QUAD:V1’, 1, pix_scale_size_um=None, xy0_off_pix=(1000,1000), do_tilt=True)
# get index arrays for pixel coordinates projected toward origin on specified zplane iX, iY = geometry.get_pixel_xy_inds_at_z(zplane=None, oname=None, oindex=0, pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True)
# get ix and iy indexes for specified point in [um]. By default p_um=(0,0) - detector origin coordinates (center). ix, iy = geometry.point_coord_indexes(p_um=(0,0)) # all other parameters should be the same as in get_pixel_coord_indexes method ix, iy = geometry.point_coord_indexes(p_um=(0,0), ‘QUAD:V1’, 1, pix_scale_size_um=None, xy0_off_pix=(1000,1000), do_tilt=True)
# get 2-d image from index arrays img = img_from_pixel_arrays(iX,iY,W=arr)
# Get specified object of the class GeometryObject, all objects are kept in the list self.list_of_geos geo = geometry.get_geo(‘QUAD:V1’, 1) # Get top GeometryObject - the object which includes all other geometry objects geo = geometry.get_top_geo()
# modify currect geometry objects’ parameters geometry.set_geo_pars(‘QUAD:V1’, 1, x0, y0, z0, rot_z, rot_y, rot_x, tilt_z, tilt_y, tilt_x) geometry.move_geo(‘QUAD:V1’, 1, 10, 20, 0) geometry.tilt_geo(‘QUAD:V1’, 1, 0.01, 0, 0)
# save current geometry parameters in file geometry.save_pars_in_file(fname_geometry_new)
# change verbosity bit-control word; to print everythisg use pbits = 0xffff geometry.set_print_bits(pbits=0)
# return geometry parameters in “psf” format as a tuple psf[32][3][3] psf = geometry.get_psf() geometry.print_psf()
See also: PSCalib.GeometryObject, PSCalib.SegGeometry, PSCalib.SegGeometryCspad2x1V1, PSCalib.SegGeometryStore
For more detail see Detector Geometry.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
$Revision: 12898 $
Version: $Id: GeometryAccess.py 12898 2016-11-22 19:27:56Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.GeometryObject¶
PSCalib.GeometryObject - building block for hierarchical geometry
Usage:
# Methods of this class are used internally in PSCalib.GeometryAccess
# and are not supposed to be used directly...
from PSCalib.GeometryObject import GeometryObject
# Instatiation of the geometry object
# d = <dictionary-of-input-parameters>
geo = GeometryObject(**d)
# test print methods:
geo.print_geo()
geo.print_geo_children()
# modification methods:
geo.set_geo_pars(self, x0, y0, z0, rot_z, rot_y, rot_x, tilt_z, tilt_y, tilt_x)
geo.move_geo(dx, dy, dz)
geo.tilt_geo(dt_x, dt_y, dt_z)
# access methods:
s = geo.str_data()
parent = geo.get_parent()
list_of_children = geo.get_list_of_children()
oname = geo.get_geo_name()
oindex = geo.get_geo_index()
pname = geo.get_parent_name()
pindex = geo.get_parent_index()
X,Y,Z = geo.get_pixel_coords(do_tilt=true)
X,Y = geo.get_2d_pixel_coords(do_tilt=true)
area = geo.get_pixel_area()
#mbits = +1-edges, +2-wide pixels, +4-non-bonded pixels, +8/+16 - four/eight neighbours of non-bonded
mask = geo.get_pixel_mask(mbits=0377)
npixels= geo.get_size_geo_array()
pixsize= geo.get_pixel_scale_size()
x0, y0, z0 = geo.get_origin()
rot_z, rot_y, rot_x = geo.get_rot()
tilt_z, tilt_y, tilt_x = geo.get_tilt()
# private methods for internal consumption:
geo.set_parent(parent)
geo.add_child(child)
Xt, Yt, Zt = geo.transform_geo_coord_arrays(X, Y, Z, do_tilt=True)
Xt, Yt = geo.transform_2d_geo_coord_arrays(X, Y, do_tilt=True)
# global methods:
Xrot, Yrot = rotation_cs(X, Y, C, S)
Xrot, Yrot = rotation(X, Y, angle_deg)
# global methods only for CSPAD2x2 array conversion between (2,185,388) and (185,388,2):
arrTwo2x1 = data2x2ToTwo2x1(asData2x2)
asData2x2 = two2x1ToData2x2(arrTwo2x1)
See also: PSCalib.GeometryAccess
For more detail see Detector Geometry.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
$Revision: 11946 $
Version: $Id: GeometryObject.py 11946 2016-05-19 00:29:37Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.GlobalUtils¶
PSCalib.GlobalUtils - contains a set of utilities
Usage:
# Import
import PSCalib.GlobalUtils as gu
# Methods
#resp = gu.<method(pars)>
dettype = gu.det_type_from_source(source)
detname = gu.string_from_source(source)
mmask = gu.merge_masks(mask1=None, mask2=None, dtype=np.uint8)
mask = gu.mask_neighbors(mask_in, allnbrs=True, dtype=np.uint8)
arr2d = gu.reshape_nda_to_2d(nda)
arr3d = gu.reshape_nda_to_3d(nda)
# Get string with time stamp, ex: 2016-01-26T10:40:53
ts = gu.str_tstamp(fmt='%Y-%m-%dT%H:%M:%S', time_sec=None)
usr = gu.get_enviroment(env='USER')
usr = gu.get_login()
host = gu.get_hostname()
cwd = gu.get_cwd()
gu.save_textfile(text, path, mode='w') # mode: 'w'-write, 'a'-append
See also: other interface methods in PSCalib.CalibPars, PSCalib.CalibParsStore
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Function PSCalib.GlobalUtils.mask_edges¶
-
PSCalib.GlobalUtils.mask_edges(mask, mrows=1, mcols=1, dtype=<type 'numpy.uint8'>)[source]¶ Return mask with a requested number of row and column pixels masked - set to 0. mask : int - n-dimensional (n>1) array with input mask mrows : int - number of edge rows to mask mcols : int - number of edge columns to mask
Module PSCalib.h5constants¶
Class PSCalib.h5constants.ConstantsLoad¶
Class PSCalib.h5constants.ConstantsStore¶
-
class
PSCalib.h5constants.ConstantsStore(obj, file)[source]¶ -
dict(d, name)[source]¶ called for every dictionary level to create a new hdf group name. it then looks into the dictionary to see if other groups need to be created
-
Function PSCalib.h5constants.save¶
-
PSCalib.h5constants.save(file, obj)[source]¶ store a constants object in an hdf5 file. the object can be a hierarchy (defined by python dictionaries) and hdf5 supported types (int, float, numpy.ndarray, string). the hierarchy can be created by having one value of a dictionary itself be a dictionary.
Module PSCalib.NDArrIO¶
PSCalib.NDArrIO - i/o methods to read/write numpy array in the text file
Usage:
# Import
from PSCalib.NDArrIO import save_txt, load_txt, list_of_comments
# Save n-dimensional numpy array in the text file.
save_txt(fname, arr, cmts=(), fmt='%.1f')
# Load 1-, 2-, n-dimensional array (if metadata available) from file .
arr = load_txt(fname) # this version unpacks data directly in this script
# or
arr = load_txt_v2(fname) # v2 uses numpy.loadtxt(...) to load data (~30% slower then the load_txt)
# Get list of str objects - comment records with '#' in 1st position from file.
cmts = list_of_comments(fname)
#------------------------------
# Example of the file header:
#------------------------------
# TITLE File to load ndarray of calibration parameters
#
# EXPERIMENT amo12345
# DETECTOR Camp.0:pnCCD.1
# CALIB_TYPE pedestals
# DATE_TIME 2014-05-06 15:24:10
# AUTHOR <user-login-name>
# line of comment always begins with #
# Mandatory fields to define the ndarray<TYPE,NDIM> and its shape as unsigned shape[NDIM] = (DIM1,DIM2,DIM3)
# DTYPE float
# NDIM 3
# DIM:1 3
# DIM:2 4
# DIM:3 8
#------------------------------
See also: Detector.AreaDetector
For more detail see AreaDetector.
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
$Revision: 12322 $
Version: $Id: NDArrIO.py 12322 2016-07-21 23:10:51Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.SegGeometry¶
SegGeometry - abstract class with interface description.
Methods of this class should be re-implemented in derived classes with name pattern SegGeometry<SensorVers>
for pixel geometry description of all sensors.
For example, CSPAD 2x1 sensor is implemented in class PSCalib.SegGeometryCspad2x1V1.
Access to all implemented sensors is available through the factory method in class PSCalib.SegGeometryStore.
Usage of interface methods:
from SegGeometryCspad2x1V1 import cspad2x1_one as sg
sg.print_seg_info(pbits=0377)
size_arr = sg.size()
rows = sg.rows()
cols = sg.cols()
shape = sg.shape()
pix_size = sg.pixel_scale_size()
area = sg.pixel_area_array()
mask = sg.pixel_mask(mbits=0377)
sizeX = sg.pixel_size_array('X')
sizeX, sizeY, sizeZ = sg.pixel_size_array()
X = sg.pixel_coord_array('X')
X,Y,Z = sg.pixel_coord_array()
xmin = sg.pixel_coord_min('X')
ymax = sg.pixel_coord_max('Y')
xmin, ymin, zmin = sg.pixel_coord_min()
xmax, ymax, zmax = sg.pixel_coord_mas()
...
print 'X.shape =', X.shape
See also: PSCalib.SegGeometry, PSCalib.SegGeometryCspad2x1V1, PSCalib.SegGeometryStore
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Revision: $Revision: 10629 $
Version: $Id: SegGeometry.py 10629 2015-08-27 23:05:30Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhail S. Dubrovin
Module PSCalib.SegGeometryCspad2x1V1¶
Class PSCalib.SegGeometryCspad2x1V1 describes the CSPAD 2x1 V1 sensor geometry.
In this class we use natural matrix notations like in data array (that is different from the DAQ notations where rows and cols are swapped).
We assume that
- 2x1 has 185 rows and 388 columns,
- X-Y coordinate system origin is in the sensor center,
- pixel (r,c)=(0,0) is in the top left corner of the matrix, has coordinates (xmin,ymax), as shown below
(Xmin,Ymax) ^ Y (Xmax,Ymax) (0,0) | (0,387) ------------------------------ | | | | | | | | | --|-------------+--------------|----> X | | | | | | | | | ------------------------------ (184,0) | (184,387) (Xmin,Ymin) (Xmax,Ymin)
Usage of interface methods:
from SegGeometryCspad2x1V1 import cspad2x1_one as sg
sg.print_seg_info(0377)
size_arr = sg.size()
rows = sg.rows()
cols = sg.cols()
shape = sg.shape()
pix_size = pixel_scale_size()
area = sg.pixel_area_array()
mask = sg.pixel_mask_array(mbits=0377)
# where mbits = +1 - edges,
# +2 - wide pixels,
# +4 - non-bonded pixels,
# +8 - nearest four neighbours of non-bonded
# +16 - eight neighbours of non-bonded
sizeX = sg.pixel_size_array('X')
sizeX, sizeY, sizeZ = sg.pixel_size_array()
X = sg.pixel_coord_array('X')
X,Y,Z = sg.pixel_coord_array()
print 'X.shape =', X.shape
xmin, ymin, zmin = sg.pixel_coord_min()
xmax, ymax, zmax = sg.pixel_coord_max()
xmin = sg.pixel_coord_min('X')
ymax = sg.pixel_coord_max('Y')
# global method for rotation of numpy arrays:
Xrot, Yrot = rotation(X, Y, C, S)
...
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
See also: PSCalib.SegGeometry
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Module PSCalib.SegGeometryEpix100V1¶
Class PSCalib.SegGeometryEpix100V1 describes the Epix100 V1 sensor geometry.
In this class we use natural matrix notations like in data array
We assume that
- 2x2 ASICs has 704 rows and 768 columns,
- Epix100 has a pixel size 50x50um, wide pixel size 50x175um
- Epix10k has a pixel size 100x100um,
- X-Y coordinate system origin is in the sensor center,
- pixel (r,c)=(0,0) is in the top left corner of the matrix, has coordinates (xmin,ymax), as shown below
(Xmin,Ymax) ^ Y (Xmax,Ymax) (0,0) | (0,768) ------------------------------ | | | | | | | | | | | | | | | | | | | | | --|-------------+--------------|----> X | | | | | | | | | | | | | | | | | | | | | ------------------------------ (704,0) | (704,768) (Xmin,Ymin) (Xmax,Ymin)
Usage of interface methods:
from SegGeometryEpix100V1 import epix2x2_one as sg
sg.print_seg_info(0377)
size_arr = sg.size()
rows = sg.rows()
cols = sg.cols()
shape = sg.shape()
pix_size = pixel_scale_size()
area = sg.pixel_area_array()
mask = sg.pixel_mask_array(mbits=0377)
# where mbits = +1-edges, +2-wide pixels
sizeX = sg.pixel_size_array('X')
sizeX, sizeY, sizeZ = sg.pixel_size_array()
X = sg.pixel_coord_array('X')
X,Y,Z = sg.pixel_coord_array()
print 'X.shape =', X.shape
xmin, ymin, zmin = sg.pixel_coord_min()
xmax, ymax, zmax = sg.pixel_coord_max()
xmin = sg.pixel_coord_min('X')
ymax = sg.pixel_coord_max('Y')
# global method for rotation of numpy arrays:
Xrot, Yrot = rotation(X, Y, C, S)
...
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
See also: PSCalib.SegGeometry
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Module PSCalib.SegGeometryMatrixV1¶
Class PSCalib.SegGeometryMatrixV1 defines the matrix V1 (pnCCD, 512x512) sensor pixel coordinates in its local frame.
Default constructor parameters are set for pnCCD; 512x512 pixels with 75x75um pixel size. In this class we use natural matrix notations like in data array (that is different from the DAQ notations where rows and cols are swapped).
We assume that
- segment has 512 rows and 512 columns,
- X-Y coordinate system origin is in the top left corner,
- ixel (r,c)=(0,0) is in the top left corner of the matrix which has coordinates (Xmin,Ymin) - is in origin.
MatrixV1 sensor coordinate frame has a matrix-style coordinate system: @code (Xmin,Ymin) (Xmin,Ymax) (0,0) (0,512) +-----------------+----> Y | | | | | | | | | | | | | | | | +-----------------+ | X V (512,0) (512,512) (Xmax,Ymin) (Xmax,Ymax) @endcode
Usage of interface methods:
from SegGeometryMatrixV1 import cspad2x1_one as sg
sg.print_seg_info(0377)
size_arr = sg.size()
rows = sg.rows()
cols = sg.cols()
shape = sg.shape()
pix_size = pixel_scale_size()
area = sg.pixel_area_array()
mask = sg.pixel_mask_array(mbits=0377)
# where mbits = +1-edges, +2-wide pixels, +4-non-bonded pixels, +8-neighbours of non-bonded
sizeX = sg.pixel_size_array('X')
sizeX, sizeY, sizeZ = sg.pixel_size_array()
X = sg.pixel_coord_array('X')
X,Y,Z = sg.pixel_coord_array()
print 'X.shape =', X.shape
xmin, ymin, zmin = sg.pixel_coord_min()
xmax, ymax, zmax = sg.pixel_coord_max()
xmin = sg.pixel_coord_min('X')
ymax = sg.pixel_coord_max('Y')
# global method for rotation of numpy arrays:
Xrot, Yrot = rotation(X, Y, C, S)
...
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
See also: PSCalib.SegGeometry
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Module PSCalib.SegGeometryStore¶
PSCalib.SegGeometryStore - is a factory class/method to switch between different device-dependent
segments/sensors to access their pixel geometry uling PSCalib.SegGeometry interface.
Usage:
from PSCalib.SegGeometryStore import sgs
sg = sgs.Create('SENS2X1:V1', pbits=0377)
sg2= sgs.Create('EPIX100:V1', pbits=0377)
sg3= sgs.Create('PNCCD:V1', pbits=0377)
sg4= sgs.Create('ANDOR3D:V1', pbits=0377)
sg.print_seg_info(pbits=0377)
size_arr = sg.size()
rows = sg.rows()
cols = sg.cols()
shape = sg.shape()
pix_size = sg.pixel_scale_size()
area = sg.pixel_area_array()
mask = sg.pixel_mask(mbits=0377)
sizeX = sg.pixel_size_array('X')
sizeX, sizeY, sizeZ = sg.pixel_size_array()
X = sg.pixel_coord_array('X')
X,Y,Z = sg.pixel_coord_array()
xmin = sg.pixel_coord_min('X')
ymax = sg.pixel_coord_max('Y')
xmin, ymin, zmin = sg.pixel_coord_min()
xmax, ymax, zmax = sg.pixel_coord_mas()
...
See also: other interface methods in PSCalib.SegGeometry, PSCalib.SegGeometryCspad2x1V1
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: 2013-03-08$
Author: Mikhail S. Dubrovin
Module PSCalib.SvnProps¶
Class SvnProps stores updated by svn properties.
NOTE: To update revision number in this file when revision changes, use command: psvn mktxtprop src/SvnProps.py or svn propset svn:keywords “Revision” src/SvnProps.py Also see: ~/.subversion/config
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Version: $Id: SvnProps.py 9205 2014-11-05 00:58:52Z dubrovin@SLAC.STANFORD.EDU $
Author: Mikhai S. Dubrovin