def modify_base_2d_instrument_group(parent, inst_nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
:param scan_type:
:return:
'''
rois = parent.get_rois_from_current_md(doc['run_start'])
dwell = parent._cur_scan_md[doc['run_start']]['dwell'] * 0.001
#det_nm = parent.get_primary_det_nm(doc['run_start'])
scan_type = parent.get_stxm_scan_type(doc['run_start'])
uid = parent.get_current_uid()
ttlpnts = int(rois[SPDB_X][NPOINTS] * rois[SPDB_Y][NPOINTS])
#det_data = np.array(parent._data['primary'][det_nm][uid]['data']) # .reshape((ynpoints, xnpoints))
#parent.make_detector(inst_nxgrp, parent._detector_names, det_data, dwell, ttlpnts, units='counts')
sample_x_data = make_1d_array(ttlpnts, parent.get_sample_x_data('start'))
sample_y_data = make_1d_array(ttlpnts, parent.get_sample_y_data('start'))
parent.make_detector(inst_nxgrp,
nxkd.SAMPLE_X,
sample_x_data,
dwell,
ttlpnts,
units='um')
parent.make_detector(inst_nxgrp,
nxkd.SAMPLE_Y,
sample_y_data,
dwell,
ttlpnts,
units='um')
if (scan_type in two_posner_scans):
xnpoints = int(rois[SPDB_X][NPOINTS])
ynpoints = int(rois[SPDB_Y][NPOINTS])
ttlpnts = int(rois[SPDB_X][NPOINTS] * rois[SPDB_Y][NPOINTS])
x_src = parent.get_devname(rois[SPDB_X][POSITIONER])
x_posnr_nm = parent.fix_posner_nm(rois[SPDB_X][POSITIONER])
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
# xdata is teh first xnpoints
xdata = parent._data['primary'][x_src][uid]['data'][0:xnpoints]
# ydata is every ynpoint
ydata = parent._data['primary'][y_src][uid]['data'][0::ynpoints]
parent.make_detector(inst_nxgrp,
y_posnr_nm,
np.tile(ydata, ynpoints),
dwell,
ttlpnts,
units='um')
parent.make_detector(inst_nxgrp,
x_posnr_nm,
np.tile(xdata, xnpoints),
dwell,
ttlpnts,
units='um')
def modify_line_spectra_instrument_group(parent, inst_nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
:param scan_type:
:return:
'''
rois = parent.get_rois_from_current_md(doc['run_start'])
dwell = parent._cur_scan_md[doc['run_start']]['dwell'] * 0.001
det_nm = parent.get_primary_det_nm(doc['run_start'])
scan_type = parent.get_stxm_scan_type(doc['run_start'])
xnpoints = dct_get(rois, SPDB_XNPOINTS)
ynpoints = dct_get(rois, SPDB_YNPOINTS)
evs = dct_get(parent._wdg_com, SPDB_SINGLE_LST_EV_ROIS)
num_ev_points = len(evs)
ttl_pnts = num_ev_points * xnpoints
evdata = np.array(evs, dtype=np.float32)
uid = parent.get_current_uid()
det_data = np.array(parent._data['primary'][det_nm][uid]['data']) # .reshape((ynpoints, xnpoints))
parent.make_detector(inst_nxgrp, parent._primary_det_prefix, det_data, dwell, ttl_pnts, units='counts')
sample_x_data = make_1d_array(ttl_pnts, parent.get_sample_x_data('start'))
sample_y_data = make_1d_array(ttl_pnts, parent.get_sample_y_data('start'))
parent.make_detector(inst_nxgrp, nxkd.SAMPLE_X, sample_x_data, dwell, ttl_pnts, units='um')
parent.make_detector(inst_nxgrp, nxkd.SAMPLE_Y, sample_y_data, dwell, ttl_pnts, units='um')
x_src = parent.get_devname(dct_get(rois, SPDB_XPOSITIONER))
x_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_XPOSITIONER))
y_src = parent.get_devname(dct_get(rois, SPDB_YPOSITIONER))
y_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_YPOSITIONER))
if (x_src not in parent._data['primary'].keys()):
# use the canned setpoints
xdata = np.array(dct_get(rois, SPDB_XSETPOINTS), dtype=np.float32)
ydata = np.array(dct_get(rois, SPDB_YSETPOINTS), dtype=np.float32)
else:
xdata = parent._data['primary'][x_src][uid]['data'][0:xnpoints]
# ydata is every ynpoint
ydata = parent._data['primary'][y_src][uid]['data'][0::num_ev_points]
if ('energy' in inst_nxgrp.keys()):
del inst_nxgrp['energy']
_dataset(inst_nxgrp, 'energy', evdata, 'NX_FLOAT')
parent.make_detector(inst_nxgrp, y_posnr_nm, np.tile(ydata, ynpoints), dwell, ttl_pnts, units='um')
parent.make_detector(inst_nxgrp, x_posnr_nm, np.tile(xdata, xnpoints), dwell, ttl_pnts, units='um')
def modify_focus_instrument_group(parent, inst_nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
:param scan_type:
:return:
'''
rois = parent.get_rois_from_current_md(doc['run_start'])
dwell = parent._cur_scan_md[doc['run_start']]['dwell'] * 0.001
det_nm = parent.get_primary_det_nm(doc['run_start'])
scan_type = parent.get_stxm_scan_type(doc['run_start'])
xnpoints = dct_get(rois, SPDB_XNPOINTS)
ynpoints = dct_get(rois, SPDB_YNPOINTS)
zznpoints = dct_get(rois, SPDB_ZZNPOINTS)
ttl_pnts = xnpoints * zznpoints
uid = parent.get_current_uid()
det_data = np.array(parent._data['primary'][det_nm][uid]
['data']) # .reshape((ynpoints, xnpoints))
parent.make_detector(inst_nxgrp,
parent._primary_det_prefix,
det_data,
dwell,
ttl_pnts,
units='counts')
sample_x_data = make_1d_array(ttl_pnts, parent.get_sample_x_data('start'))
sample_y_data = make_1d_array(ttl_pnts, parent.get_sample_y_data('start'))
parent.make_detector(inst_nxgrp,
nxkd.SAMPLE_X,
sample_x_data,
dwell,
ttl_pnts,
units='um')
parent.make_detector(inst_nxgrp,
nxkd.SAMPLE_Y,
sample_y_data,
dwell,
ttl_pnts,
units='um')
x_src = parent.get_devname(dct_get(rois, SPDB_XPOSITIONER))
x_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_XPOSITIONER))
y_src = parent.get_devname(dct_get(rois, SPDB_YPOSITIONER))
y_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_YPOSITIONER))
zz_src = parent.get_devname(dct_get(rois, SPDB_ZZPOSITIONER))
zz_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_ZZPOSITIONER))
# xdata is teh first xnpoints
if (x_src not in parent._data['primary'].keys()):
# use the canned setpoints
xdata = np.array(dct_get(rois, SPDB_XSETPOINTS), dtype=np.float32)
ydata = np.array(dct_get(rois, SPDB_YSETPOINTS), dtype=np.float32)
zzdata = np.array(dct_get(rois, SPDB_ZZSETPOINTS), dtype=np.float32)
else:
xdata = parent._data['primary'][x_src][uid]['data'][0:xnpoints]
# ydata is every ynpoint
ydata = parent._data['primary'][y_src][uid]['data'][0::zznpoints]
zzdata = parent._data['primary'][zz_src][uid]['data'][0::ynpoints]
parent.make_detector(inst_nxgrp,
y_posnr_nm,
np.tile(ydata, ynpoints),
dwell,
ttl_pnts,
units='um')
parent.make_detector(inst_nxgrp,
x_posnr_nm,
np.tile(xdata, xnpoints),
dwell,
ttl_pnts,
units='um')
parent.make_detector(inst_nxgrp,
zz_posnr_nm,
np.tile(zzdata, zznpoints),
dwell,
ttl_pnts,
units='um')
def modify_spectra_nxdata_group(parent, data_nxgrp, doc, scan_type):
'''
:param parent:
:param data_nxgrp:
:param doc:
:param scan_type:
:return:
'''
resize_data = False
rois = parent.get_rois_from_current_md(doc['run_start'])
x_src = parent.get_devname(rois[SPDB_X][POSITIONER])
x_posnr_nm = parent.fix_posner_nm(rois[SPDB_X][POSITIONER])
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
evs = dct_get(parent._wdg_com, SPDB_SINGLE_LST_EV_ROIS)
num_ev_points = len(evs)
xnpoints = int(rois[SPDB_X][NPOINTS])
ynpoints = int(rois[SPDB_Y][NPOINTS])
ttlpnts = xnpoints * num_ev_points
uid = parent.get_current_uid()
#primary_det_nm = parent.get_primary_det_nm(uid)
det_nm = data_nxgrp.name.split('/')[-1]
det_data = np.array(parent._data['primary'][det_nm][uid]['data'],
dtype=np.float32)
det_data = det_data[0::len(parent._sp_id_lst)]
rows = 1
cols, = det_data.shape
if ((rows * cols) < ttlpnts):
#scn had been aborted
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(xnpoints, dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
else:
if (x_src not in parent._data['primary'].keys()):
xdata = make_1d_array(ttlpnts, rois[SPDB_X][SETPOINTS])
ydata = make_1d_array(ttlpnts, rois[SPDB_Y][SETPOINTS])
else:
# use actual data
# xdata is teh first xnpoints
#xdata = np.array(parent._data['primary'][x_src][uid]['data'][0:xnpoints], dtype=np.float32)
xdata = make_1d_array(ttlpnts, parent.get_sample_x_data('start'))
# ydata is every ynpoint
#ydata = np.array(parent._data['primary'][y_src][uid]['data'][0::ynpoints], dtype=np.float32)
ydata = make_1d_array(ttlpnts, parent.get_sample_y_data('start'))
#regardless of the positioner, these names (sample_x, sample_y) are hardcoded into the nxstxm definition
# if there were already sample_x and y created by the default constructors then delete them and recreate with the right data
if (nxkd.SAMPLE_Y in data_nxgrp.keys()):
del (data_nxgrp[nxkd.SAMPLE_X])
del (data_nxgrp[nxkd.SAMPLE_Y])
_dataset(data_nxgrp, nxkd.SAMPLE_Y, ydata, 'NX_FLOAT')
_dataset(data_nxgrp, nxkd.SAMPLE_X, xdata, 'NX_FLOAT')
#_string_attr(data_nxgrp, 'axes', [y_posnr_nm, x_posnr_nm])
_string_attr(data_nxgrp, 'axes', ['energy', nxkd.SAMPLE_Y, nxkd.SAMPLE_X])
_string_attr(data_nxgrp, 'signal', 'data')
#_dataset(data_nxgrp, 'data', prim_data_arr, 'NX_NUMBER')
_dset = _dataset(data_nxgrp, 'data', det_data, 'NX_NUMBER')
_string_attr(_dset, 'signal', '1')
def modify_spectra_instrument_group(parent, inst_nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
:param scan_type:
:return:
'''
rois = parent.get_rois_from_current_md(doc['run_start'])
dwell = parent._cur_scan_md[doc['run_start']]['dwell'] * 0.001
#det_nm = parent.get_primary_det_nm(doc['run_start'])
scan_type = parent.get_stxm_scan_type(doc['run_start'])
xnpoints = int(rois[SPDB_X][NPOINTS])
ynpoints = int(rois[SPDB_Y][NPOINTS])
evs = dct_get(parent._wdg_com, SPDB_SINGLE_LST_EV_ROIS)
num_ev_points = len(evs)
ttlpnts = xnpoints * num_ev_points
uid = parent.get_current_uid()
#det_data = np.array(parent._data['primary'][det_nm][uid]['data']) # .reshape((ynpoints, xnpoints))
#parent.make_detector(inst_nxgrp, det_nm, det_data, dwell, ttlpnts, units='counts')
sample_x_data = make_1d_array(ttlpnts, parent.get_sample_x_data('start'))
sample_y_data = make_1d_array(ttlpnts, parent.get_sample_y_data('start'))
parent.make_detector(inst_nxgrp,
nxkd.SAMPLE_X,
sample_x_data,
dwell,
ttlpnts,
units='um')
parent.make_detector(inst_nxgrp,
nxkd.SAMPLE_Y,
sample_y_data,
dwell,
ttlpnts,
units='um')
#if (scan_type in two_posner_scans):
# xnpoints = int(rois[SPDB_X][NPOINTS])
# ynpoints = int(rois[SPDB_Y][NPOINTS])
# ttlpnts = xnpoints * ynpoints
x_src = parent.get_devname(rois[SPDB_X][POSITIONER])
x_posnr_nm = parent.fix_posner_nm(rois[SPDB_X][POSITIONER])
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
# xdata is teh first xnpoints
if (x_src not in parent._data['primary'].keys()):
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
else:
xdata = parent._data['primary'][x_src]['data'][0:xnpoints]
# ydata is every ynpoint
ydata = parent._data['primary'][y_src]['data'][0::ynpoints]
parent.make_detector(inst_nxgrp,
y_posnr_nm,
np.tile(ydata, ynpoints),
dwell,
ttlpnts,
units='um')
parent.make_detector(inst_nxgrp,
x_posnr_nm,
np.tile(xdata, xnpoints),
dwell,
ttlpnts,
units='um')