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Adjust the mask parameters using editor window and click on "Apply" button again. Mask image will have changed according to set parameters.

Geometry and Detector Image

Command to test

ami-local -b 1 -f interval=1 psana://exp=uedcom103,run=7,dir=/cds/data/psdm/prj/public01/xtc

Use geometry with image

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Select optional geometry file

By default geometry data comes from DB associated with experiment or detector. Optional geometry file can be specified through the click on Geometry Control Node to deal with parameters window.

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Click on "select" button and select desired geometry file, e.g.

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Use Geometry without input array

Add the Geometry Control Node as usually and remove input terminal for arr3d. Click on "Apply" and use any geometry output parameters except "image".

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RoiArch

Simple example

In simple case we use 2D image as input array without mask and ImageViewer with bin numbers in stead of actual scales for radial and angular dimensions.

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Image can be moved and zoomed by click-and-drag and scrolling mouse, respectfullyrespectively.

ArchROI can be adjusted using 3 control points for center, external radius and entire rotation, internal radius and arch angular size. Alternatively, ArchRoi parameters can be adjusted using editor for parameters in the left side of the window. Click on "Apply" button after mask parameters are set.

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Then build other control nodes as in previous examples, click on "Apply" button, etc.

Geometry and Detector Image

RoiArch output for 2-d mask

ami-local -b 1 -f interval=1 psana://exp=tmoc00118,run=222,dir=/cds/data/psdm/prj/public01/xtc

• NEW: Node RoiArch got new output terminal Mask (Array2d)
• Use tmo_opal1:raw:image (Array2d) as input to RoiArch, draw/edit arch, get Mask (Array2d) shaped as input image.

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Usage of RoiArch for multi-panel detector and make 2-d and 3-d masks

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Code Block
title Command to test GeometryTest command
ami-local -b 1 -f interval=1 psana://exp=uedcom103,run=7,dir=/cds/data/psdm/prj/public01/xtc

Use geometry with image

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Select optional geometry file

By default geometry data comes from DB associated with experiment or detector. Optional geometry file can be specified through the click on Geometry Control Node to deal with parameters window.

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Click on "select" button and select desired geometry file, e.g.

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Use Geometry without input array

Add the Geometry Control Node as usually and remove input terminal for arr3d. Click on "Apply" and use any geometry output parameters except "image".

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PythonEditor for calib components

NEW:

• in node Geometry separate arrays are combined in lists of index and coordinate arrays
• new nodes Mask3dFrom2d and TableFromArr3d

Example shows how to

• use epixquad:raw:raw (Array3d) and epixquad:calibconst (dict) as input to Geometry to generate image (Array2d),
• pass this image to RoiArch input, draw/edit arch, get Mask (Array2d) shaped as input image,
• use node Mask3dFrom2d with input mask2d from RoiArch and inds_xy from Geometry to generate 3-d mask array shaped as raw data,
• use nodes TableFromArr3d to convert 3-d mask to 2-d table of segments (without Geometry) to plot with ImageViewer.1

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Potential extension of the node Geometry for 3-d mask output (TEMPORARY FOR PRESENTATION ONLY)

AMI issues

• Mask 3-d can be converted directly in the node Geometry (Mask3dFrom2d may not be required...),
  • it needs in optional input parameters
• AMI does not work correctly with default input terminals
  • unused terminals must be remover interactively
  • if intermediate terminal removed input is moved to previous one...
• Also need in a few parameters in TableFromArr3d, but
  • AMI fails to pickle qt modules (ComboBox, etc) and crashes...

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Example of issue with pickle of qt object

Essential code is in ami/flowchart/library/Psalg.py

ami-local -b 1 -f interval=1 psana://exp=uedcom103,run=7,dir=/cds/data/psdm/prj/public01/xtc

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Crash:

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...

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PythonEditor for calib components of epix10ka and epixhr detectors

This example shows how to access in ami all components of the det.raw.calib(...) method such as calibration constants, per-panel trbit and asicPixelConfig, per-event gain factors and pedestals, mask, common mode correction, etc.

 AMI test command

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for epixquad and epixhr

# for epixquad - 4-panel epix10ka:
ami-local -b 1 -f interval=1 psana://exp=ueddaq02,run=569,dir=/cds/data/psdm/prj/public01/xtc

# for single panel epixhr:
ami-local -b 1 -f interval=1 psana://exp=rixx45619,run=121,dir=/cds/data/psdm/prj/public01/xtc

Composition of Control Nodes for example

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Implementation of the class calib_componenyts

• Module detector/utils_ami.py will be available in releases grater than ps-4.5.24.
• It is implemented for epix10ka and epixhr detector types.
• Code example is also available in the head of this module.
• Common mode correction methods are not available yet in this example.

Code example for PythonEditor

In this example the PythonEditor box receives input objects for raw (np.ndarray), config, calibconst, accesses and prints internal components of the det.raw.calib(...) method and returns 2-d image for one retrieved arrays. For imaging, the 3-d array of common mode correction is converted to 2-d table of segments. 

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import psana.detector.utils_amicalib_components as ua

 ucc

np, info_ndarr, table_nxn_epix10ka_from_ndarr =\
  ucc.np, ucc.info_ndarr, ucc.psu.table_nxn_epix10ka_from_ndarr


class EventProcessor():

    def __init__(self):
        self.counter = 0
        self.cc = None
 
    def begin_run(self):
        pass

    def end_run(self):
        pass

    def begin_step(self, step):
        pass

    def end_step(self, step):
        pass
     
    def on_event(self, raw, config, calibconst, *args, **kwargs):
        self.counter += 1
        if self.cc is None:
            self.cc = uaucc.calib_components_epix(calibconst, config)
        cc = self.cc

        kwa = {'status': True}
        cmpars = (0, 7, 300, 10)

        ctypes   = cc.calib_types() # list of calibration types
        npanels  = cc.number_of_panels() # number of panels/segments in the detector
        peds     = cc.pedestals() # OR cc.calib_constants('pedestals')
        gain     = cc.gain()      # OR cc.calib_constants('pixel_gain') # ADU/keV
        gfactor  = cc.gain_factor() # keV/ADU
        status   = cc.status() # 4-d array of pixel_status constants
        comode   = cc.common_mode()  # tuple of common mode correction parameters
        trbit_p0 = cc.trbit_for_panel(0)  # list of per-ASIC trbit for panel 0
        ascfg_p0 = cc.asicPixelConfig_for_panel(0) # matrix of asicPixelConfig for panel 0
        mask     = cc.mask(status=True)**kwa) # mask defined by kwa
        dettype  = cc.dettype() # detector type, e.g.  "epix10ka" or "epixhr"
        cbitscfg = cc.cbits_config_detector()
        cbitstot = cc.cbits_config_and_data_detector(raw, cbitscfg)
        gmaps   gmap = cc.gain_maps_epix10ka_anyepix(raw) # gain map
        pedest  peds_ev = cc.event_pedestals(raw) # per-pixel array of pedestals in the event
        factor gfac_ev  = cc.event_gain_factor(raw) # per-pixel array of gain factors in the event
        calib0  calib = cc.calib(raw, cmpars=(0, 7, 300, 10))**kwa) # method calib
        cmcorr   = cc.common_mode_correction(raw, cmpars=(0, 7, 300, 10))
cmpars, **kwa) # common mode correction
        arrf = np.array(raw & cc.data_bit_mask(), dtype=np.float32) - pedest

        print('== Event %04d ==' % self.counter)
#        print('config', cc.config)
#        print('calib_typesmetadata', ctypescc.calib_metadata('pedestals'))
#        print('calib_metadatatypes', cc.calib_metadata('pedestals')ctypes)
        print(ua.info_ndarr(peds, 'pedestals'))
        print(ua.info_ndarr(cc.gain(), 'gain'))
        print(ua.info_ndarr(gfactor, 'gain_factor'))
        print(ua.info_ndarr(status, 'status'))
        print('common_mode from caliconst', str(comode))        
        print('number_of_panels', npanels)
        print('trbit_for_panel(0)', trbit_p0)
        print(ua.info_ndarr(ascfg_p0, 'asicPixelConfig_for_panel(0)'))
        print(ua.info_ndarr(raw, 'raw'))
        print(ua.info_ndarr(mask, 'mask'))
        print('dettype', dettype)
        print(ua.info_ndarr(cbitscfg, 'cbitscfg'))
        print(ua.info_ndarr(cbitstot, 'cbitstot'))
        print(ua.info_ndarr(gmapgmaps, 'gmapgmaps'))
        print(ua.info_ndarr(peds_ev, 'peds_ev(pedest, 'pedest'))
        print(info_ndarr(factor, 'factor'))
        print(info_ndarr(cmcorr, 'cmcorr'))
        print(ua.info_ndarr(gfac_ev(arrf, 'raw(data bits)-peds'))
        print(info_ndarr(calib0, 'gfac_ev')calib0'))

        # det.raw.calib(...) algorithm close reproduction
        calib1 = None
        if True:
            arrf1 = arrf.copy()
            cc.common_mode_apply(arrf1, gmaps, cmpars=cmpars, **kwa)
        print(ua.    calib1 = arrf1 * factor if mask is None else arrf1 * factor * mask
            print(info_ndarr(calibcalib1, 'calibcalib1'))

        # print(ua.det.raw.calib(...) - effective algorithm
        calib2 = None
        if True:
            arrf2 = arrf.copy() + cmcorr
            calib2 = arrf2 * factor if mask is None else arrf2 * factor * mask
            print(info_ndarr(cmcorrcalib2, 'cmcorrcalib2'))

        # img = cmcorr[0, 144:, :192]
        # img = ua.psu.table_nxn_epix10ka_from_ndarr(cmcorr)
        img = table_nxn_epix10ka_from_ndarr(calib1)
        print(ua.info_ndarr(img, 'img'))
        return img

Composition of Control Nodes in the example

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Image for common mode correction and calib1, respectively

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Implementation of the class calib_components_epix

• Module detector/utils_calib_components.py will be available in releases grater than ps-4.5.24.
• It is implemented for epix10ka and epixhr detector types.
• Code example is also available in the head of this module.

Test example in psana

Example shows how to initialize and use the calib_components_epix object using parameters retrieved from the detector interface.

This script can be executed in the lcls2 psana environment by the command like

python ./lcls2/psana/psana/detector/test_issues_2023.py 2

References

• ami
• Area Detector Interface
• Area detector mask examples

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