PSCalib documentation¶
Class GeometryObject is a building block for hierarchical geometry¶
Usage:
# Methods of this class are used internally in :py:class:`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 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.
Author: Mikhail Dubrovin
-
GeometryObject.data2x2ToTwo2x1(arr2x2)[source]¶ Converts array shaped as CSPAD2x2 data (185,388,2) to two 2x1 arrays with shape=(2,185,388)
-
GeometryObject.rotation(X, Y, angle_deg)[source]¶ For numpy arrays X and Y returns the numpy arrays of Xrot and Yrot rotated by angle_deg
Class 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 next-line-symbol 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:
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.
Author: Mikhail Dubrovin
-
class
GeometryAccess.GeometryAccess(path=None, pbits=0)[source]¶ -
-
__init__(path=None, pbits=0)[source]¶ Constructor of the class
GeometryAccessParameters
- path : str - path to the geometry file
- pbits : int - verbosity bitword
-
get_pixel_areas(oname=None, oindex=0)[source]¶ Returns pixel areas array for top or specified geometry object
-
get_pixel_coord_indexes(oname=None, oindex=0, pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True)[source]¶ Returns two pixel X,Y coordinate index arrays for top or specified geometry object
-
get_pixel_coords(oname=None, oindex=0, do_tilt=True)[source]¶ Returns three pixel X,Y,Z coordinate arrays for top or specified geometry object
-
get_pixel_mask(oname=None, oindex=0, mbits=255, **kwargs)[source]¶ Returns pixel mask array for top or specified geometry object.
- mbits =+1 - mask edges
- +2 - two wide-pixel central columns +4 - non-bonded pixels +8 - four nearest neighbours of non-bonded pixels +16- eight neighbours of non-bonded pixels
-
get_pixel_scale_size(oname=None, oindex=0)[source]¶ Returns pixel scale size for top or specified geometry object
-
get_pixel_xy_at_z(zplane=None, oname=None, oindex=0, do_tilt=True)[source]¶ Returns pixel coordinate arrays XatZ, YatZ, for specified zplane and geometry object.
This method projects pixel X, Y coordinates in 3-D on the specified Z plane along direction to origin.
-
get_pixel_xy_inds_at_z(zplane=None, oname=None, oindex=0, pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True)[source]¶ Returns pixel coordinate index arrays iX, iY of size for specified zplane and geometry object
-
get_psf()[source]¶ Returns array of vectors in TJ format (psf stands for position-slow-fast vectors)
-
load_pars_from_file(path=None)[source]¶ Reads input “geometry” file, discards empty lines and comments, fills the list of geometry objects for data lines
-
load_pars_from_str(s)[source]¶ Reads input geometry from str, discards empty lines and comments, fills the list of geometry objects for data lines
-
move_geo(oname=None, oindex=0, dx=0, dy=0, dz=0)[source]¶ Moves specified or top geometry object by dx, dy, dz
-
point_coord_indexes(p_um=(0, 0), oname=None, oindex=0, pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True)[source]¶ Converts point (x_um, y_um) corrdinates [um] to pixel (ix, iy) indexes. All other parameters are the same as in get_pixel_coord_indexes. WARNING: indexes are not required to be inside the image. They are integer, may be negative or exceed pixel maximal index.
-
print_pixel_coords(oname=None, oindex=0)[source]¶ Partial print of pixel coordinate X,Y,Z arrays for selected or top(by default) geo
-
-
GeometryAccess.divide_protected(num, den, vsub_zero=0)[source]¶ Returns result of devision of numpy arrays num/den with substitution of value vsub_zero for zero den elements.
-
GeometryAccess.img_default(shape=(10, 10), dtype=<type 'numpy.float32'>)[source]¶ Returns default image
-
GeometryAccess.img_from_pixel_arrays(iX, iY, W=None, dtype=<type 'numpy.float32'>, vbase=0)[source]¶ Returns image from iX, iY coordinate index arrays and associated weights W.
-
GeometryAccess.test_access(geometry)[source]¶ Tests geometry acess methods of the class GeometryAccess
-
GeometryAccess.test_mask_quad(geometry, mbits)[source]¶ Tests geometry acess methods of the class GeometryAccess object for CSPAD quad
-
GeometryAccess.test_plot_cspad(geometry, fname_data, amp_range=(0, 0.5))[source]¶ The same test as previous, but use get_pixel_coord_indexes(…) method
Class SegGeometryStore is a factory class/method¶
Switches between different device-dependent segments/sensors
to access their pixel geometry using 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)
sg5= sgs.Create('JUNGFRAU: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:
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.
Created: 2013-03-08 by Mikhail Dubrovin
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:
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:
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.
Author: Mikhail Dubrovin
Class 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:
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)
...
- See:
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.
Created: 2013-03-08 by Mikhail Dubrovin
-
class
SegGeometryCspad2x1V1.SegGeometryCspad2x1V1(sp, use_wide_pix_center=True)[source]¶ Bases:
PSCalib.SegGeometry.SegGeometrySelf-sufficient class for generation of CSPad 2x1 sensor pixel coordinate array
-
make_pixel_coord_arrs(sp)[source]¶ Makes [185,388] maps of x, y, and z 2x1 pixel coordinates with origin in the center of 2x1
-
pixel_coord_array(sp, axis=None)[source]¶ Returns numpy array of segment pixel coordinates in um for AXIS
-
pixel_coord_max(sp, axis=None)[source]¶ Returns maximal value in the array of segment pixel coordinates in um for AXIS
-
pixel_coord_min(sp, axis=None)[source]¶ Returns minimal value in the array of segment pixel coordinates in um for AXIS
-
pixel_mask_array(sp, mbits=255)[source]¶ Returns numpy array of pixel mask: 1/0 = ok/masked, mbits=1 - mask edges, +2 - mask two central columns, +4 - mask non-bonded pixels, +8 - mask nearest four neighbours of nonbonded pixels, +16- mask eight neighbours of nonbonded pixels.
-
Class 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) | (0,767) ------------------------------ | | | | | | | | | | | | | | | | | | | | | --|-------------+--------------|----> X | | | | | | | | | | | | | | | | | | | | | ------------------------------ (703,0) | (703,767) (Xmin,Ymin) (Xmax,Ymin)
Usage:
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)
...
- See:
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.
Created: 2013-03-08 by Mikhail Dubrovin
-
class
SegGeometryEpix100V1.SegGeometryEpix100V1(sp, use_wide_pix_center=True)[source]¶ Bases:
PSCalib.SegGeometry.SegGeometrySelf-sufficient class for generation of Epix100 2x2 sensor pixel coordinate array
-
make_pixel_coord_arrs(sp)[source]¶ Makes [704,768] maps of x, y, and z 2x2 pixel coordinates with origin in the center of 2x2
-
pixel_coord_array(sp, axis=None)[source]¶ Returns numpy array of segment pixel coordinates in um for AXIS
-
pixel_coord_max(sp, axis=None)[source]¶ Returns maximal value in the array of segment pixel coordinates in um for AXIS
-
pixel_coord_min(sp, axis=None)[source]¶ Returns minimal value in the array of segment pixel coordinates in um for AXIS
-
pixel_mask_array(sp, mbits=255)[source]¶ Returns numpy array of pixel mask: 1/0 = ok/masked, mbits: +1 - mask edges, +2 - mask two central columns
-
Class 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) (0,511) +-----------------+----> Y | | | | | | | | | | | | | | | | +-----------------+ | X V (511,0) (511,511) (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)
...
- See:
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.
Created: 2013-03-08 by Mikhail Dubrovin
-
class
SegGeometryMatrixV1.SegGeometryMatrixV1(sp, rows=512, cols=512, pix_size_rows=75, pix_size_cols=75, pix_size_depth=400, pix_scale_size=75)[source]¶ Bases:
PSCalib.SegGeometry.SegGeometrySelf-sufficient class for generation of CSPad 2x1 sensor pixel coordinate array
-
pixel_coord_array(sp, axis=None)[source]¶ Returns numpy array of segment pixel coordinates in um for AXIS
-
pixel_coord_max(sp, axis=None)[source]¶ Returns maximal value in the array of segment pixel coordinates in um for AXIS
-
pixel_coord_min(sp, axis=None)[source]¶ Returns minimal value in the array of segment pixel coordinates in um for AXIS
-
pixel_mask_array(sp, mbits=255)[source]¶ Returns numpy array of pixel mask: 1/0 = ok/masked, mbits=1 - mask edges, +2 - mask two central columns, +4 - mask non-bonded pixels, +8 - mask nearest neighbours of nonbonded pixels.
-
Class SegGeometryJungfrauV1 describes the Jungfrau V1 sensor geometry¶
Data array for Jungfrau 512x1024 segment is shaped as (1,512,1024), has a matrix-like numeration for rows and columns with gaps between 2x4 ASICs
We assume that
- 1x1 ASICs has 256 rows and 256 columns,
- Jungfrau has a pixel size 75x75um
- 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) | (0,1023) ----------------- -----------------|----------------- ----------------- | | | ||| | | | | ASIC | | ||| | | | | 256x256 | | ||| | | | | | | ||| | | | | | | ||| | | | | | | ||| | | | ----------------- -----------------|----------------- ----------------- -------------------------------------+-------------------------------------> X ----------------- -----------------|----------------- ----------------- | | | ||| | | | | | | ||| | | | | | | ||| | | | | | | ||| | | | | | | ||| | | | | | | ||| | | | ----------------- -----------------|----------------- ----------------- (511,0) | (1023,1023) (Xmin,Ymin) (Xmax,Ymin)
Usage:
from PSCalib.SegGeometryJungfrauV1 import jungfrau_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, width=1)
# 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)
...
- See:
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.
Created: 2017-10-12 by Mikhail Dubrovin
-
class
SegGeometryJungfrauV1.SegGeometryJungfrauV1(sp)[source]¶ Bases:
PSCalib.SegGeometry.SegGeometrySelf-sufficient class for generation of Jungfrau 2x4 sensor pixel coordinate array
-
make_pixel_coord_arrs(sp)[source]¶ Makes [512,1024] maps of x, y, and z pixel coordinates with origin in the center of 2x4
-
pixel_coord_array(sp, axis=None)[source]¶ Returns numpy array of segment pixel coordinates in um for AXIS
-
pixel_coord_max(sp, axis=None)[source]¶ Returns maximal value in the array of segment pixel coordinates in um for AXIS
-
pixel_coord_min(sp, axis=None)[source]¶ Returns minimal value in the array of segment pixel coordinates in um for AXIS
-
pixel_mask_array(sp, mbits=255, width=1)[source]¶ Returns numpy array of pixel mask: 1/0 = ok/masked,
Parameters
- mbits:
- +1 - mask edges, +2 - mask central columns
width (uint) - width in pixels of masked edge
-
DCMethods is a set of utilities for direct operations with calibration data¶
Usage:
# Import
import psana
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'
ds = psana.DataSource(dsname)
env=ds.env()
evt=ds.events().next()
src = 'Cspad.' # 'Epix100a.', etc
ctype = gu.PIXEL_MASK # | 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'
par = evt # psana.Event | float - tsec event time
parts = env # psana.Env | psana.Event | float - tsec event time
# Methods with dynamically-reconstructed calib file name
dcm.add_constants(nda, par, env, src='Epix100a.', ctype=gu.PIXEL_MASK, calibdir=None, vers=None, pred=None, succ=None, cmt=None, verb=False)
dcm.print_content(env, src='Epix100a.', calibdir=None)
nda = dcm.get_constants(par, env, src='Epix100a.', ctype=gu.PIXEL_MASK, calibdir=None, vers=None, verb=False)
dcm.delete_version(evt, env, src='Epix100a.', ctype=gu.PIXEL_MASK, calibdir=None, vers=None, cmt=None, verb=False)
dcm.delete_range (evt, env, src='Epix100a.', ctype=gu.PIXEL_MASK, calibdir=None, range=None, cmt=None, verb=False)
dcm.delete_ctype (evt, env, src='Epix100a.', ctype=gu.PIXEL_MASK, calibdir=None, cmt=None, verb=False)
# Methods using fname
dcm.add_constants_to_file(data, fname, parts, env, ctype=gu.PIXEL_MASK, vers=None, pred=None, succ=None, cmt=None, verb=False)
dcm.print_content_from_file(fname)
nda = dcm.get_constants_from_file(fname, parts, ctype=gu.PIXEL_MASK, vers=None, verb=False)
dcm.delete_version_from_file(fname, parts, ctype=gu.PIXEL_MASK, vers=None, cmt=None, verb=False)
dcm.delete_range_from_file (fname, ctype=gu.PIXEL_MASK, range=None, cmt=None, verb=False)
dcm.delete_ctype_from_file (fname, ctype=gu.PIXEL_MASK, cmt=None, verb=False)
- Methods
- Classes:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016-09-23 by Mikhail Dubrovin
-
DCMethods.add_constants(data, par, 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 -> hdf5 file name
- par : psana.Event | float time -> event time
- src : str - source short/full name, alias or full -> hdf5 file name
- 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
See
DCMethods
-
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 | psana.Env | float - tsec event time
- env : psana.Env -> is used to get exp=env.experiment() for comments etc.
- 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 print any message
See
DCMethods
-
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
See
DCMethods
-
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
See
DCMethods
-
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
See
DCMethods
-
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
See
DCMethods
-
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
See
DCMethods
-
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 | psana.Env | 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
See
DCMethods
-
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 - to get 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
Return
numpy.array - array of calibratiopn constatnts.
See
DCMethods
-
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 | psana.Env | float - tsec event time
- ctype : gu.CTYPE - enumerated calibration type, e.g.: gu.PIXEL_MASK
- vers : int - calibration version
Returns
- np.array - specified array of calibration constants
See
DCMethods
-
DCMethods.is_good_fname(fname, verb=False)[source]¶ Checks the hdf5 file name validity, returns True or False.
Parameters
- fname : str - full path to the file
- verb : bool - verbosity, default=False - do not print any message
Returns
True/False - for existing or not file
-
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)
See
DCMethods
Class DCStore 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016 by Mikhail Dubrovin
Class DCBase is a 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
-
class
DCBase.DCBase(cmt=None)[source]¶ Bases:
objectBase class for the Detector Calibration (DC) project.
Parameters
cmt : str - string of comment associated with derived class object.
-
__weakref__¶ list of weak references to the object (if defined)
-
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.
-
Class DCType 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016 by Mikhail Dubrovin
-
class
DCType.DCType(ctype, cmt=None)[source]¶ Bases:
PSCalib.DCInterface.DCTypeIClass for the Detector Calibration (DC) project
Parameters
ctype : gu.CTYPE - enumerated calibration type cmt : str - comment
Class DCRange 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016-09-23 at Mikhail Dubrovin
Class DCVersion 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016 by Mikhail Dubrovin
DCInterface - abstract interface for the Detector Calibration (DC) project¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
-
class
DCInterface.DCRangeI(begin, end, cmt=None)[source]¶ Bases:
PSCalib.DCBase.DCBaseAbstract 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
DCInterface.DCStoreI(fname, cmt=None)[source]¶ Bases:
PSCalib.DCBase.DCBaseAbstract 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
DCInterface.DCTypeI(ctype, cmt=None)[source]¶ Bases:
PSCalib.DCBase.DCBaseAbstract 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
DCInterface.DCVersionI(vnum, tsprod=None, arr=None, cmt=None)[source]¶ Bases:
PSCalib.DCBase.DCBaseAbstract 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.
Class 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() # e.g., epix100a
did = o.detid() # e.g., 3925868555
dn = o.detname() # e.g., epix100a-3925868555
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/d/psdm/detector/calib/epix100a/
fpath = o.calib_file_path_repo() # e.g., /reg/d/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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
-
class
DCFileName.DCFileName(env, src, calibdir=None)[source]¶ File name generator object for Detector Calibration Store (DCS) project.
Parameters
evt : psana.Event -> event time 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)
-
calib_file_dir_repo()[source]¶ Returns repository directory, e.g.: /reg/d/psdm/detector/calib/epix100a/
-
calib_file_path_repo()[source]¶ Returns path to the file in repository, e.g.: /reg/d/…/calib/epix100a/epix100a-3925868555.h5
-
Class DCDetectorId 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
-
DCDetectorId.id_cspad(env, src)[source]¶ Returns detector full name for any src, e.g., XppGon.0:Cspad2x2.0
DCConfigParameters - class supporting configuration parameters for application¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment. Created: 2016-05-17 by Mikhail Dubrovin
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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
Class DCLogger - logger for Detector Calibration Store¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016-05-17 by Mikhail Dubrovin
Class 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)
fid = gu.evt_fiducials(evt)
t_sec = gu.evt_time(evt)
t_sec = gu.env_time(env)
# 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:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2016 by Mikhail Dubrovin
-
DCUtils.detector_full_name(env, src)[source]¶ Returns full detector name like ‘XppGon.0:Cspad2x2.0’ for short src, alias src, or psana.Source.
-
DCUtils.dettype_from_str_source(src)[source]¶ Returns the detector type from full psana source name (Ex.: Cspad2x2 from DetInfo(XppGon.0:Cspad2x2.0)
-
DCUtils.get_enviroment(env='USER')[source]¶ Returns the value of specified by string name environment variable
-
DCUtils.get_subgroup(grp, subgr_name)[source]¶ For hdf5: returns subgroup of the group if it exists or creates and returns new subgroup
-
DCUtils.par_to_tsec(par)[source]¶ Checks if par is float or assumes that it is psana.Event and returns event time in (float) sec or None.
Parameters
- par : psana.Event | psana.Env | float - tsec event time | None
Returns
event time in (float) sec or None.
-
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
-
DCUtils.save_object_as_dset(grp, name, shape=None, dtype=None, data=0)[source]¶ Saves object as h5py dataset
Currently supports scalar int, double, string and numpy.array
-
DCUtils.save_string_as_dset(grp, name, s)[source]¶ Creates and returns the h5py dataset object with name for single string s
-
DCUtils.source_full_name(env, src)[source]¶ Returns full name like ‘DetInfo(XppGon.0:Cspad2x2.0)’ of the brief source or its alias using env.configStore().keys()
Class 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)
See GlobalUtils, NDArrIO
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
-
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
-
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
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: 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.
Author: Mikhail Dubrovin
-
NDArrIO.list_of_comments(fname)[source]¶ Returns list of str objects - comment records from file. - fname - file name for text file.
-
NDArrIO.load_txt(fname)[source]¶ Reads n-dimensional numpy array from text file with metadata. - fname - file name for text file.
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 CalibParsCspadV1
which enherits from CalibPars, etc.
Currently implementation of this interface for all detectors is done in class GenericCalibPars.
Access to all detectors is available through the factory method in class 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_datast()
size = cp.pixel_rms()
size = cp.pixel_gain()
size = cp.pixel_offset()
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)
- Methods:
print_attrs()pedestals()pixel_status()pixel_datast()pixel_rms()pixel_gain()pixel_offset()pixel_mask()pixel_bkgd()common_mode()ndim()shape()size()status()
- See classes:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsStore - a factory class/method¶
Switches between different device-dependent calibration constants using CalibPars 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_datast()
nda = o.pixel_rms()
nda = o.pixel_mask()
nda = o.pixel_gain()
nda = o.pixel_offset()
nda = o.pixel_bkgd()
nda = o.common_mode()
status = o.status(ctype=PEDESTALS) # see list of ctypes in :py:class:`GlobalUtils`
shape = o.shape(ctype)
size = o.size(ctype)
ndim = o.ndim(ctype)
- Methods:
Create()CreateForEvtEnv()
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2013-03-08 by Mikhail Dubrovin
-
class
CalibParsStore.CalibParsStore[source]¶ Factory class for CalibPars object of different detectors
-
Create(calibdir, group, source, runnum, pbits=0, fnexpc=None, fnrepo=None, tsec=None)[source]¶ Factory method
Parameters
- calibdir : string - calibration directory, ex: /reg/d/psdm/AMO/amoa1214/calib
- group : string - group, ex: PNCCD::CalibV1
- source : string - data source, ex: Camp.0:pnCCD.0
- runnum : int - run number, ex: 10
- pbits=0 : int - print control bits, ex: 255
Returns
- GenericCalibPars object
-
CreateForEvtEnv(calibdir, group, source, par, env, pbits=0)[source]¶ Factory method This method makes access to the calibration store with fallback access to hdf5 file.
Parameters
- calibdir : string - calibration directory, ex: /reg/d/psdm/AMO/amoa1214/calib
- group : string - group, ex: PNCCD::CalibV1
- source : string - data source, ex: Camp.0:pnCCD.0
- par : int runnum or psana.Event - is used to get run number
- env : psana.Env - environment object - is used to retrieve file name to get dataset time to retrieve DCRange
- pbits=0 : int - print control bits, ex: 255
Returns
- GenericCalibPars object
-
Class 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_datast()
nda = gcp.pixel_gain()
nda = gcp.pixel_offset()
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 CalibPars, CalibParsStore, CalibParsCspad2x1V1, GlobalUtils
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsBaseAcqirisV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
Class CalibParsBaseAndor3dV1 holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsBaseAndorV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail S. Dubrovin
Class CalibParsBaseCameraV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsBaseCSPad2x2V1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
Class CalibParsBaseCSPadV1 holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsBaseEpix100aV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
Class CalibParsBaseImpV1 holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsBaseJungfrauV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
Class CalibParsBasePnccdV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
CalibParsBasePrincetonV1 - holds basic calibration metadata parameters for associated detector¶
- See:
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Author: Mikhail Dubrovin
GlobalUtils - 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)
lo,hi = gu.evaluate_limits(arr, nneg=5, npos=5, lim_lo=1, lim_hi=1000, verbos=1, cmt='')
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()
rec = gu.log_rec_on_start() # e.g. '2017-09-27T10:40:24 user:dubrovin@psanagpu104 cwd:/reg/neh/home4/dubrovin/LCLS/con-jungfrau ...'
gu.add_rec_to_log(lfname, rec, verbos=False)
exp = gu.exp_name(env)
cdir = gu.calib_dir(env)
#### tsec, tnsec, fiducial, tsdate, tstime = gu.time_pars(evt) # needs in psana...
gu.create_directory(dir, verb=False)
gu.create_directory_with_mode(dir, mode=0777, verb=False)
exists = gu.create_path(path, depth=6, mode=0777, verb=True)
arr = gu.load_textfile(path)
gu.save_textfile(text, path, mode='w') # mode: 'w'-write, 'a'-append
path = gu.replace('/path/#YYYY-MM/fname.txt', '#YYYY-MM', gu.str_tstamp(fmt='%Y/%m'))
ifname = 'fname.txt'
ctypedir = '/some-path/calib/Jungfrau::CalibV1/CxiEndstation.0:Jungfrau.0/'
ctype = 'pedestals'
ofname = '123-end.data'
rec = gu.history_record(ifname, ctypedir, ctype, ofname, comment='')
path_clb = gu.path_to_calib_file(ctypedir, ctype, ofname)
path_his = gu.path_to_history_file(ctypedir, ctype)
cmd = gu.command_deploy_file(ifname, path_clb)
cmd = gu.command_add_record_to_file(rec, path_his)
tpl = gu.calib_fname_template(exp, runnum, tsec, tnsec, fid, tsdate, tstime, src, nevts, ofname)
gu.deploy_file(ifname, ctypedir, ctype, ofname, lfname=None, verbos=False)
See: other methods in CalibPars, CalibParsStore
This software was developed for the SIT project. If you use all or part of it, please give an appropriate acknowledgment.
Created: 2013-03-08 by Mikhail Dubrovin
-
GlobalUtils.ZYLA= 27¶ Enumetated detector types
-
GlobalUtils.add_rec_to_log(lfname, rec, verbos=False)[source]¶ Adds record rec to the log file with path lfname. If path does not exist, it is created beginning from depth=5.
-
GlobalUtils.calib_fname_template(exp, runnum, tsec, tnsec, fid, tsdate, tstime, src, nevts, ofname)[source]¶ Replaces parts of the file name ofname specified as #src, #exp, #run, #evts, #type, #date, #time, #fid, #sec, #nsec with actual values.
RETURNS
- template (str) - file name template, e.g.: nda-cxi11216-r0009-CxiEndstation.0:Jungfrau.0-e000010-%s.txt,
- where %s stands for supplied late type.
-
GlobalUtils.command_deploy_file(ifname, ofname)[source]¶ Returns command to deploys file with calibration constants in the calib store.
-
GlobalUtils.create_directory_with_mode(dir, mode=511, verb=False)[source]¶ Creates directory and sets its mode
-
GlobalUtils.create_path(path, depth=6, mode=511, verb=False)[source]¶ Creates missing path of specified depth from the beginning e.g. for ‘/reg/g/psdm/logs/calibman/2016/07/log-file-name.txt’ or ‘/reg/d/psdm/cxi/cxi11216/calib/Jungfrau::CalibV1/CxiEndstation.0:Jungfrau.0/pedestals/9-end.data’
Returns True if path to file exists, False othervise
-
GlobalUtils.deploy_file(ifname, ctypedir, ctype, ofname, lfname=None, verbos=False)[source]¶ Deploys file with calibration constants in the calib store, adds history record in file and in logfile.
Parameters
- ifname : str - input file name, e.g.: ‘fname.txt’
- ctypedir : str - path to calibtype directory, e.g. ‘/some-path/calib/Jungfrau::CalibV1/CxiEndstation.0:Jungfrau.0/’
- ctype : str - calibration type, e.g.: ‘pedestals’
- ofname : str - output file name, e.g.: ‘123-end.data’
- lfname : str - log file path or None, to add history record
- verbos : bool - verbosity
-
GlobalUtils.det_type_from_source(source)[source]¶ Returns enumerated detector type for string source
-
GlobalUtils.dic_det_type_to_calib_group= {0: 'UNDEFINED', 1: 'CsPad::CalibV1', 2: 'CsPad2x2::CalibV1', 3: 'Princeton::CalibV1', 4: 'PNCCD::CalibV1', 5: 'Camera::CalibV1', 6: 'Camera::CalibV1', 7: 'Camera::CalibV1', 8: 'Camera::CalibV1', 9: 'Camera::CalibV1', 10: 'Camera::CalibV1', 11: 'Epix::CalibV1', 12: 'Epix10k::CalibV1', 13: 'Epix100a::CalibV1', 14: 'Camera::CalibV1', 15: 'Andor::CalibV1', 16: 'Acqiris::CalibV1', 17: 'Imp::CalibV1', 18: 'Camera::CalibV1', 19: 'Camera::CalibV1', 20: 'EvrData::CalibV1', 21: 'Camera::CalibV1', 22: 'Timepix::CalibV1', 23: 'Fli::CalibV1', 24: 'Pimax::CalibV1', 25: 'Andor3d::CalibV1', 26: 'Jungfrau::CalibV1', 27: 'Camera::CalibV1'}¶ Dictionary for detector type : group
-
GlobalUtils.dic_det_type_to_name= {0: 'UNDEFINED', 1: 'Cspad', 2: 'Cspad2x2', 3: 'Princeton', 4: 'pnCCD', 5: 'Tm6740', 6: 'Opal1000', 7: 'Opal2000', 8: 'Opal4000', 9: 'Opal8000', 10: 'OrcaFl40', 11: 'Epix', 12: 'Epix10k', 13: 'Epix100a', 14: 'Fccd960', 15: 'Andor', 16: 'Acqiris', 17: 'Imp', 18: 'Quartz4A150', 19: 'Rayonix', 20: 'Evr', 21: 'Fccd', 22: 'Timepix', 23: 'Fli', 24: 'Pimax', 25: 'Andor3d', 26: 'Jungfrau', 27: 'Zyla'}¶ Dictionary for detector type : name
-
GlobalUtils.evaluate_limits(arr, nneg=5, npos=5, lim_lo=1, lim_hi=1000, verbos=1, cmt='')[source]¶ Evaluates low and high limit of the array, which are used to find bad pixels.
-
GlobalUtils.get_enviroment(env='USER')[source]¶ Returns the value of specified by string name environment variable
-
GlobalUtils.history_record(ifname, ctypedir, ctype, ofname, comment='')[source]¶ Returns (str) history record about deployed constants.
Parameters
- ifname : str - input file name, e.g.: ‘fname.txt’
- ctypedir : str - path to calibtype directory, e.g. ‘/some-path/calib/Jungfrau::CalibV1/CxiEndstation.0:Jungfrau.0/’
- ctype : str - calibration type, e.g.: ‘pedestals’
- ofname : str - output file name, e.g.: ‘123-end.data’
- comment : str - any comment
- verbos : bool - verbosity
-
GlobalUtils.list_of_calib_groups= ('UNDEFINED', 'CsPad::CalibV1', 'CsPad2x2::CalibV1', 'Princeton::CalibV1', 'PNCCD::CalibV1', 'Camera::CalibV1', 'Camera::CalibV1', 'Camera::CalibV1', 'Camera::CalibV1', 'Camera::CalibV1', 'Camera::CalibV1', 'Epix::CalibV1', 'Epix10k::CalibV1', 'Epix100a::CalibV1', 'Camera::CalibV1', 'Andor::CalibV1', 'Acqiris::CalibV1', 'Imp::CalibV1', 'Camera::CalibV1', 'Camera::CalibV1', 'EvrData::CalibV1', 'Camera::CalibV1', 'Timepix::CalibV1', 'Fli::CalibV1', 'Pimax::CalibV1', 'Andor3d::CalibV1', 'Jungfrau::CalibV1', 'Camera::CalibV1')¶ List of enumetated detector calibration groups
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GlobalUtils.list_of_det_names= ('UNDEFINED', 'Cspad', 'Cspad2x2', 'Princeton', 'pnCCD', 'Tm6740', 'Opal1000', 'Opal2000', 'Opal4000', 'Opal8000', 'OrcaFl40', 'Epix', 'Epix10k', 'Epix100a', 'Fccd960', 'Andor', 'Acqiris', 'Imp', 'Quartz4A150', 'Rayonix', 'Evr', 'Fccd', 'Timepix', 'Fli', 'Pimax', 'Andor3d', 'Jungfrau', 'Zyla')¶ List of enumetated detector names
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GlobalUtils.list_of_det_type= (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27)¶ List of enumetated detector types
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GlobalUtils.log_rec_on_start()[source]¶ Returns (str) record containing timestamp, login, host, cwd, and command line
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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
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GlobalUtils.mask_neighbors(mask, allnbrs=True, dtype=<type 'numpy.uint8'>)[source]¶ Return mask with masked eight neighbor pixels around each 0-bad pixel in input mask.
mask : int - n-dimensional (n>1) array with input mask allnbrs : bool - False/True - masks 4/8 neighbor pixels.
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GlobalUtils.merge_masks(mask1=None, mask2=None, dtype=<type 'numpy.uint8'>)[source]¶ Merging masks using np.logical_and rule: (0,1,0,1)^(0,0,1,1) = (0,0,0,1)
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GlobalUtils.path_to_calib_file(ctypedir, ctype, ofname)[source]¶ Returns path to file wirh calibration constants in the calib store. e.g. /some-path/calib/Jungfrau::CalibV1/CxiEndstation.0:Jungfrau.0/pedestals/9-end.data See parameters description in
history_record().
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GlobalUtils.path_to_history_file(ctypedir, ctype)[source]¶ Returns path to HISTORY file in the calib store. e.g. /some-path/calib/Jungfrau::CalibV1/CxiEndstation.0:Jungfrau.0/pedestals/HYSTORY See parameters description in
history_record().
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GlobalUtils.replace(template, pattern, subst)[source]¶ If pattern in the template replaces it with subst. Returns str object template with replaced patterns.
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GlobalUtils.save_textfile(text, path, mode='w')[source]¶ Saves text in file specified by path. mode: ‘w’-write, ‘a’-append
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RunProcUtils.append_log_file(exp='xpptut15', procname='pixel_status', runs=[], verb=0)[source]¶ Appends records in the log file for list of (str) runs for specified experiment and process name.
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RunProcUtils.arc_file(exp='xpptut15', procname='pixel_status')[source]¶ Returns (str) arcive log file name, e.g. ‘/reg/g/psdm/logs/run_proc/pixel_status/CXI/xpptut15-proc-arch.txt’
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RunProcUtils.control_file(procname='pixel_status')[source]¶ Returns (str) control file name, e.g. ‘/reg/g/psdm/logs/run_proc/pixel_status/proc_control.txt’
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RunProcUtils.dict_exp_run_old(ins='CXI', procname='pixel_status')[source]¶ Returns dict {exp:list_of_runs} for specified instrument (=None for all) and procname, e.g. {‘mfx13016’:[‘0005’,‘0006’], ‘mfx15070’:[‘0003’,‘0004’,‘0005’],…]
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RunProcUtils.exp_run_new(ins='CXI', procname='pixel_status')[source]¶ Returns new list of tuples (exp,run) for specified instrument (=None for all) and procname, e.g. [(‘mfx13016’,‘0005’), (‘mfx15070’,‘0008’),…]
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RunProcUtils.exp_run_new_under_control(procname='pixel_status')[source]¶ Returns new list of tuples (exp,run) for specified procname for experiments from control file, e.g. [(‘mfx13016’,‘0005’), (‘mfx15070’,‘0008’),…]
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RunProcUtils.exp_run_old(ins='CXI', procname='pixel_status')[source]¶ Returns old list of tuples (exp,run) for specified instrument (=None for all) and procname, e.g. [(‘mfx13016’,‘0005’), (‘mfx15070’,‘0008’),…]
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RunProcUtils.experiments(ins='CXI')[source]¶ Returns list of (8,9-char-str) experiment names for specified 3-char (str) instrument name, or all experiments is ins=None, e.g. [‘mfxo1916’, ‘mfxn8416’, ‘mfxlq3915’,…]
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RunProcUtils.experiments_under_control(procname='pixel_status')[source]¶ Returns list of (str) experiment names from control file.
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RunProcUtils.log_file(exp='xpptut15', procname='pixel_status')[source]¶ Returns (str) log file name, e.g. ‘/reg/g/psdm/logs/run_proc/pixel_status/CXI/xpptut15-proc-runs.txt’
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RunProcUtils.move_recs_to_archive(procname, exp, runs)[source]¶ Move expired run records from log file to archive file.
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RunProcUtils.msg_to_log(runs=[])[source]¶ Returns (str) message to the log file for list of (str) runs.
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RunProcUtils.recs_in_log_file(exp='xpptut15', procname='pixel_status', verb=0)[source]¶ Returns list of (str) records in the log file for specified experiment and process name. E.g. of one record: ‘0151 2017-10-05T15:19:21’
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RunProcUtils.runs_in_log_file(exp='xpptut15', procname='pixel_status')[source]¶ Returns list of (4-char str) runs in the log file for specified experiment and process name. E.g. [‘0059’, ‘0060’,…]
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RunProcUtils.runs_in_xtc_dir(exp='xpptut15', verb=0)[source]¶ Returns sorted list of (str) runs in xtc directory name, e.g. [‘0059’, ‘0060’,…]
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RunProcUtils.runs_new_in_exp(exp='xpptut15', procname='pixel_status', verb=0)[source]¶ Returns list of (4-char str) runs which are found in xtc directory and not yet listed in the log file, e.g. [‘0059’, ‘0060’,…]
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RunProcUtils.runs_old_in_exp(exp='xpptut15', procname='pixel_status', verb=0)[source]¶ Returns list of (4-char str) runs which are found in the log file and are not listed in xtc directory, e.g. [‘0059’, ‘0060’,…]
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RunProcUtils.xtc_dir(exp='xpptut15')[source]¶ Returns (str) xtc directory name, e.g. ‘/reg/d/psdm/XPP/xpptut15/xtc’
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SubprocUtils.subproc(cmd, env=None, shell=False)[source]¶ e.g., command=’bsub -q psananehq -o log-ls.txt ls -l] command_seq=[‘bsub’, ‘-q’, cp.batch_queue, ‘-o’, ‘log-ls.txt’, ‘ls -l’]