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_generic_scan_nxdata_group(parent, data_nxgrp, doc, scan_type):
'''
:param entry_nxgrp:
:param cntr_nm:
: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])
xnpoints = int(rois[SPDB_X][NPOINTS])
ttlpnts = xnpoints
uid = parent.get_current_uid()
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
else:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
_dataset(data_nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
_string_attr(data_nxgrp, 'axes', [x_posnr_nm])
_string_attr(data_nxgrp, 'signal', 'data')
det_nm = data_nxgrp.name.split('/')[-1]
# det_data = np.array(self._data['primary'][det_nm]['data'], dtype=np.float32).reshape((ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'],
dtype=np.float32)
_dset = _dataset(data_nxgrp, 'data', det_data, 'NX_NUMBER')
_string_attr(_dset, 'signal', '1')
def modify_generic_scan_ctrl_data_grps(parent, nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
: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])
xnpoints = rois[SPDB_X][NPOINTS]
ttlpnts = xnpoints
uid = parent.get_current_uid()
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X]['SETPOINTS'], dtype=np.float32)
else:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
_dataset(nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
# this should be an array the same shape as the 'data' group in NXdata filled with the storagering current
sr_data = np.array(
parent._data['primary'][parent.get_devname(DNM_RING_CURRENT) +
'_val'][uid]['data'],
dtype=np.float32)
if (resize_data):
sr_data = np.resize(sr_data, (ttlpnts, ))
_dataset(nxgrp, 'data', sr_data, 'NX_NUMBER')
modify_generic_scan_ctrl_str_attrs(parent, nxgrp, doc)
def modify_spectra_ctrl_data_grps(parent, nxgrp, doc, scan_type):
'''
:param parent:
:param 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])
xnpoints = int(rois[SPDB_X][NPOINTS])
ynpoints = int(rois[SPDB_Y][NPOINTS])
evs = parent._wdg_com['SINGLE_LST']['EV_ROIS']
num_ev_points = len(evs)
ttlpnts = num_ev_points * xnpoints * ynpoints
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
# _dataset(nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
# _dataset(nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
#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 nxgrp.keys()):
del (nxgrp[nxkd.SAMPLE_X])
del (nxgrp[nxkd.SAMPLE_Y])
# these names (sample_x, sample_y) are hardcoded into the nxstxm definition
_dataset(nxgrp, nxkd.SAMPLE_Y, ydata, 'NX_FLOAT')
_dataset(nxgrp, nxkd.SAMPLE_X, xdata, 'NX_FLOAT')
# this should be an array the same shape as the 'data' group in NXdata filled with the storagering current
_sr_data = parent.get_baseline_all_data(
parent.get_devname(DNM_RING_CURRENT))
sr_data = np.linspace(_sr_data[0], _sr_data[1], ttlpnts)
_dataset(nxgrp, 'data',
np.reshape(sr_data, (num_ev_points, ynpoints, xnpoints)),
'NX_NUMBER')
modify_spectra_ctrl_str_attrs(parent, nxgrp, doc)
def modify_single_image_ctrl_data_grps(parent, nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
: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])
# x_posnr_src = rois[SPDB_X]['SRC']
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
# y_posnr_src = rois[SPDB_Y]['SRC']
xnpoints = int(rois[SPDB_X][NPOINTS])
ynpoints = int(rois[SPDB_Y][NPOINTS])
ttlpnts = xnpoints * ynpoints
# uid = list(parent._cur_scan_md.keys())[0]
# primary_det_nm = parent.get_primary_det_nm(uid)
# prim_data_lst = parent._data['primary'][primary_det_nm]['data']
# if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
# else:
# # use actual data
# # xdata is teh first xnpoints
# xdata = np.array(parent._data['primary'][x_src]['data'][0:xnpoints], dtype=np.float32)
# # ydata is every ynpoint
# ydata = np.array(parent._data['primary'][y_src]['data'][0::ynpoints], dtype=np.float32)
_dataset(nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
# this should be an array the same shape as the 'data' group in NXdata filled with the storagering current
_sr_data = parent.get_baseline_all_data(
parent.get_devname(DNM_RING_CURRENT))
sr_data = np.linspace(_sr_data[0], _sr_data[1], ttlpnts)
#if (resize_data):
# sr_data = np.resize(sr_data, (ttlpnts,))
_dataset(nxgrp, 'data', np.reshape(sr_data, (ynpoints, xnpoints)),
'NX_NUMBER')
modify_single_image_ctrl_str_attrs(parent, nxgrp, doc)
def modify_focus_ctrl_data_grps(parent, nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
:return:
'''
resize_data = False
rois = parent.get_rois_from_current_md(doc['run_start'])
x_src = parent.get_devname(dct_get(rois, SPDB_XPOSITIONER))
x_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_XPOSITIONER))
# x_posnr_src = rois['X']['SRC']
y_src = parent.get_devname(dct_get(rois, SPDB_YPOSITIONER))
y_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_YPOSITIONER))
# y_posnr_src = rois['Y']['SRC']
uid = parent.get_current_uid()
zz_src = parent.get_devname(dct_get(rois, SPDB_ZZPOSITIONER))
zz_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_ZZPOSITIONER))
xnpoints = dct_get(rois, SPDB_XNPOINTS)
ynpoints = dct_get(rois, SPDB_YNPOINTS)
znpoints = dct_get(rois, SPDB_ZZNPOINTS)
ttlpnts = xnpoints * znpoints
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:
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
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:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(
parent._data['primary'][y_src][uid]['data'][0::znpoints],
dtype=np.float32)
zzdata = np.array(
parent._data['primary'][zz_src][uid]['data'][0::ynpoints],
dtype=np.float32)
_dataset(nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
_dataset(nxgrp, zz_posnr_nm, zzdata, 'NX_FLOAT')
# this should be an array the same shape as the 'data' group in NXdata filled with the storagering current
ring_cur_signame = parent.get_devname(DNM_RING_CURRENT) + '_val'
if (ring_cur_signame not in parent._data.keys()):
#use the baseline start/stop values and create a sequence from start to stop
strt, stp = parent._data['baseline'][ring_cur_signame][uid]['data']
sr_data = np.linspace(strt, stp, ttlpnts, endpoint=True)
else:
sr_data = np.array(
parent._data['baseline'][ring_cur_signame][uid]['data'],
dtype=np.float32)
if (resize_data):
sr_data = np.resize(sr_data, (ttlpnts, ))
_dataset(nxgrp, 'data', np.reshape(sr_data, (znpoints, xnpoints)),
'NX_NUMBER')
modify_focus_ctrl_str_attrs(parent, nxgrp, doc)
def modify_focus_nxdata_group(parent, data_nxgrp, doc, scan_type):
'''
:param entry_nxgrp:
:param cntr_nm:
:param doc:
:param scan_type:
:return:
'''
resize_data = False
rois = parent.get_rois_from_current_md(doc['run_start'])
x_src = parent.get_devname(dct_get(rois, SPDB_XPOSITIONER))
x_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_XPOSITIONER))
# x_posnr_src = rois['X']['SRC']
y_src = parent.get_devname(dct_get(rois, SPDB_YPOSITIONER))
y_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_YPOSITIONER))
# y_posnr_src = rois['Y']['SRC']
zz_src = parent.get_devname(dct_get(rois, SPDB_ZZPOSITIONER))
zz_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_ZZPOSITIONER))
uid = parent.get_current_uid()
xnpoints = dct_get(rois, SPDB_XNPOINTS)
ynpoints = dct_get(rois, SPDB_YNPOINTS)
zznpoints = dct_get(rois, SPDB_ZZNPOINTS)
ttl_pnts = xnpoints * zznpoints
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:
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttl_pnts):
resize_data = True
# scan was aborted so use setpoint data here
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:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(
parent._data['primary'][y_src][uid]['data'][0::zznpoints],
dtype=np.float32)
zzdata = np.array(
parent._data['primary'][zz_src][uid]['data'][0::ynpoints],
dtype=np.float32)
_dataset(data_nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(data_nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
_dataset(data_nxgrp, zz_posnr_nm, zzdata, 'NX_FLOAT')
_string_attr(data_nxgrp, 'axes', [zz_posnr_nm, y_posnr_nm, x_posnr_nm])
_string_attr(data_nxgrp, 'signal', 'data')
det_nm = parent.get_primary_det_nm(doc['run_start'])
three_d_scans = [scan_types.OSA_FOCUS.value, scan_types.SAMPLE_FOCUS.value]
if (scan_types(scan_type) in three_d_scans):
# det_data = np.array(parent._data['primary'][det_nm]['data'], dtype=np.float32).reshape((1, ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'])
# if(len(det_data) > ttl_pnts):
# det_data = np.array(parent._data['primary'][det_nm][uid]['data'][0:zznpoints][0:xnpoints], dtype=np.float32)
# elif(len(det_data) < ttl_pnts):
# print('modify_focus_nxdata_group: NEED TO PAD THE DATA, length should be %d but is %d' % (len(det_data), ttl_pnts))
if (resize_data):
det_data = parent.fix_aborted_data(det_data, ttl_pnts)
det_data = np.reshape(det_data, (1, zznpoints, xnpoints))
else:
# det_data = np.array(parent._data['primary'][det_nm]['data'], dtype=np.float32).reshape((ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'],
dtype=np.float32)
_dataset(data_nxgrp, 'data', det_data, 'NX_NUMBER')
def modify_base_2d_nxdata_group(parent, data_nxgrp, doc, scan_type):
'''
:param entry_nxgrp:
:param cntr_nm:
: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])
uid = parent.get_current_uid()
xnpoints = int(rois[SPDB_X][NPOINTS])
ynpoints = int(rois[SPDB_Y][NPOINTS])
ttlpnts = xnpoints * ynpoints
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
else:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(
parent._data['primary'][y_src][uid]['data'][0::ynpoints],
dtype=np.float32)
_dataset(data_nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(data_nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
_string_attr(data_nxgrp, 'axes', [y_posnr_nm, x_posnr_nm])
_string_attr(data_nxgrp, 'signal', 'data')
#det_nm = parent.get_primary_det_nm(doc['run_start'])
det_nm = data_nxgrp.name.split('/')[-1]
three_d_scans = [scan_types.DETECTOR_IMAGE, scan_types.OSA_IMAGE, scan_types.OSA_FOCUS, scan_types.SAMPLE_FOCUS, scan_types.SAMPLE_IMAGE_STACK, \
scan_types.COARSE_IMAGE, scan_types.COARSE_GONI, scan_types.TOMOGRAPHY]
if (scan_types(scan_type) in three_d_scans):
# det_data = np.array(parent._data['primary'][det_nm]['data'], dtype=np.float32).reshape((1, ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'],
dtype=np.float32)
if (resize_data):
det_data = parent.fix_aborted_data(det_data, ttlpnts)
det_data = np.reshape(det_data, (1, ynpoints, xnpoints))
if (MARK_DATA):
# put a black box in corner
c = int(xnpoints / 3)
r = int(xnpoints / 3)
for n in range(r):
det_data[0, n, 0:c] = 0
else:
# det_data = np.array(parent._data['primary'][det_nm]['data'], dtype=np.float32).reshape((ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'],
dtype=np.float32)
_dset = _dataset(data_nxgrp, 'data', det_data, 'NX_NUMBER')
_string_attr(_dset, 'signal', '1')
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_stack_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])
# x_posnr_src = rois[SPDB_X]['SRC']
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
# y_posnr_src = rois[SPDB_Y]['SRC']
xnpoints = rois[SPDB_X]['NPOINTS']
ynpoints = rois[SPDB_Y]['NPOINTS']
ttlpnts = xnpoints * ynpoints
#prim_data_lst = parent._data['primary'][x_src]['data']
#uid = list(parent._cur_scan_md.keys())[0]
uid = parent.get_current_uid()
primary_det_nm = parent.get_primary_det_nm(uid)
#prim_data_lst = parent._data['primary'][primary_det_nm]['data']
prim_data_arr = np.array(
parent._data['primary'][primary_det_nm][uid]['data'])
if (scan_types(scan_type) is scan_types.SAMPLE_POINT_SPECTRA):
rows = 1
cols, = prim_data_arr.shape
else:
rows, cols = prim_data_arr.shape
if ((rows * cols) < ttlpnts):
#scn had been aborted
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
else:
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:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(
parent._data['primary'][y_src][uid]['data'][0::ynpoints],
dtype=np.float32)
# _dataset(data_nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
# _dataset(data_nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
#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')
det_nm = parent.get_primary_det_nm(doc['run_start'])
#need to find out how many energy points we need to make space for
det_data = np.array(parent._data['primary'][det_nm][uid]['data'],
dtype=np.float32)
#js_str = parent._cur_scan_md[doc['run_start']]['wdg_com']
#wdg_com = json.loads(js_str)
evs = parent._wdg_com['SINGLE_LST']['EV_ROIS']
num_ev_points = len(evs)
rows, cols = det_data.shape
#init_dat_arr = np.zeros((num_ev_points, rows, cols), dtype=np.float32)
init_dat_arr = np.empty((num_ev_points, rows, cols), dtype=np.float32)
init_dat_arr[:] = np.NAN
init_dat_arr[0] = det_data
_dataset(data_nxgrp, 'data', init_dat_arr, 'NX_NUMBER')
def modify_single_image_nxdata_group(parent, data_nxgrp, doc, scan_type):
'''
:param entry_nxgrp:
:param cntr_nm:
: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])
# x_posnr_src = rois[SPDB_X]['SRC']
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
# y_posnr_src = rois[SPDB_Y]['SRC']
xnpoints = rois[SPDB_X][NPOINTS]
ynpoints = rois[SPDB_Y][NPOINTS]
ttlpnts = xnpoints * ynpoints
#prim_data_lst = parent._data['primary'][x_src]['data']
#uid = list(parent._cur_scan_md.keys())[0]
uid = parent.get_current_uid()
primary_det_nm = parent.get_primary_det_nm(uid)
prim_data_arr = np.array(parent._data['primary'][primary_det_nm][uid]['data'])
if(scan_types(scan_type) is scan_types.PATTERN_GEN_SCAN):
rows, cols = ynpoints, xnpoints
else:
rows, cols = prim_data_arr.shape
#rows, cols = prim_data_arr.shape
if ((rows * cols) < ttlpnts):
#scn had been aborted
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
else:
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:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(parent._data['primary'][x_src][uid]['data'][0:xnpoints], dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(parent._data['primary'][y_src][uid]['data'][0::ynpoints], dtype=np.float32)
_dataset(data_nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(data_nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
_string_attr(data_nxgrp, 'axes', [y_posnr_nm, x_posnr_nm])
_string_attr(data_nxgrp, 'signal', 'data')
det_nm = parent.get_primary_det_nm(doc['run_start'])
# three_d_scans = [scan_types.DETECTOR_IMAGE, scan_types.OSA_IMAGE, scan_types.OSA_FOCUS, scan_types.SAMPLE_FOCUS, scan_types.SAMPLE_IMAGE_STACK, \
# scan_types.COARSE_IMAGE_SCAN, scan_types.COARSE_GONI_SCAN, scan_types.TOMOGRAPHY_SCAN]
three_d_scans = [scan_types.DETECTOR_IMAGE, scan_types.OSA_IMAGE, scan_types.OSA_FOCUS, scan_types.SAMPLE_FOCUS, \
scan_types.COARSE_IMAGE_SCAN, scan_types.COARSE_GONI_SCAN, scan_types.TOMOGRAPHY_SCAN]
if(scan_types(scan_type) in three_d_scans):
# det_data = np.array(parent._data['primary'][det_nm]['data'], dtype=np.float32).reshape((1, ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'], dtype=np.float32)
if (resize_data):
det_data = parent.fix_aborted_data(det_data, ttlpnts)
det_data = np.reshape(det_data, (1, ynpoints, xnpoints))
if(MARK_DATA):
# put a black box in corner
c = int(xnpoints / 3)
r = int(xnpoints / 3)
for n in range(r):
det_data[0, n, 0:c] = 0
else:
# det_data = np.array(parent._data['primary'][det_nm]['data'], dtype=np.float32).reshape((ynpoints, xnpoints))
det_data = np.array(parent._data['primary'][det_nm][uid]['data'], dtype=np.float32)
_dataset(data_nxgrp, 'data', det_data, 'NX_NUMBER')
def modify_line_spectra_nxdata_group(parent, data_nxgrp, doc, scan_type):
'''
:param entry_nxgrp:
:param cntr_nm:
:param doc:
:param scan_type:
:return:
'''
resize_data = False
rois = parent.get_rois_from_current_md(doc['run_start'])
x_src = parent.get_devname(dct_get(rois, SPDB_XPOSITIONER))
x_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_XPOSITIONER))
# x_posnr_src = rois['X']['SRC']
y_src = parent.get_devname(dct_get(rois, SPDB_YPOSITIONER))
y_posnr_nm = parent.fix_posner_nm(dct_get(rois, SPDB_YPOSITIONER))
uid = parent.get_current_uid()
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)
evdata = np.array(evs, dtype=np.float32)
ttlpnts = num_ev_points * 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)
else:
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(dct_get(rois, SPDB_XSETPOINTS), dtype=np.float32)
ydata = np.array(dct_get(rois, SPDB_YSETPOINTS), dtype=np.float32)
else:
# use actual data
# xdata is the first xnpoints
xdata = np.array(parent._data['primary'][x_src][uid]['data'][0:xnpoints], dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(parent._data['primary'][y_src][uid]['data'][0::num_ev_points], dtype=np.float32)
xstart = dct_get(rois, SPDB_XSTART)
xstop = dct_get(rois, SPDB_XSTOP)
xstep = dct_get(rois, SPDB_XSTEP)
ls_dat = np.linspace(xstart, xstop + xstep, num=xnpoints + 1, endpoint=True)
line_position = np.cumsum(np.diff(ls_dat))
_dataset(data_nxgrp, 'line_position', line_position, 'NX_FLOAT')
_dataset(data_nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(data_nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
if('energy' in data_nxgrp.keys()):
del data_nxgrp['energy']
_dataset(data_nxgrp, 'energy', evdata, 'NX_FLOAT')
_string_attr(data_nxgrp, 'axes', ['energy', 'line_position'])
_string_attr(data_nxgrp, 'signal', 'data')
det_nm = parent.get_primary_det_nm(doc['run_start'])
det_data = np.array(parent._data['primary'][det_nm][uid]['data'], dtype=np.float32)
if (resize_data):
det_data = parent.fix_aborted_data(det_data, ttlpnts)
det_data = np.transpose(det_data)
_dataset(data_nxgrp, 'data', det_data, 'NX_NUMBER')
def modify_line_spectra_ctrl_data_grps(parent, nxgrp, doc, scan_type):
'''
:param nxgrp:
:param doc:
:return:
'''
resize_data = False
rois = parent.get_rois_from_current_md(doc['run_start'])
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))
uid = parent.get_current_uid()
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)
evdata = np.array(evs, dtype=np.float32)
ttlpnts = num_ev_points * 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)
else:
prim_data_lst = parent._data['primary'][x_src][uid]['data']
if (len(prim_data_lst) < ttlpnts):
resize_data = True
# scan was aborted so use setpoint data here
xdata = np.array(dct_get(rois, SPDB_XSETPOINTS), dtype=np.float32)
ydata = np.array(dct_get(rois, SPDB_YSETPOINTS), dtype=np.float32)
else:
# use actual data
# xdata is the first xnpoints
xdata = np.array(parent._data['primary'][x_src][uid]['data'][0:xnpoints], dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(parent._data['primary'][y_src][uid]['data'][0::ynpoints], dtype=np.float32)
xstart = dct_get(rois, SPDB_XSTART)
xstop = dct_get(rois, SPDB_XSTOP)
xstep = dct_get(rois, SPDB_XSTEP)
ls_dat = np.linspace(xstart, xstop + xstep, num=xnpoints + 1, endpoint=True)
line_position = np.cumsum(np.diff(ls_dat))
_dataset(nxgrp, 'line_position', line_position, 'NX_FLOAT')
_dataset(nxgrp, y_posnr_nm, ydata, 'NX_FLOAT')
_dataset(nxgrp, x_posnr_nm, xdata, 'NX_FLOAT')
if ('energy' in nxgrp.keys()):
del nxgrp['energy']
_dataset(nxgrp, 'energy', evdata, 'NX_FLOAT')
# this should be an array the same shape as the 'data' group in NXdata filled with the storagering current
ring_cur_signame = parent.get_devname(DNM_RING_CURRENT) + '_val'
if(ring_cur_signame not in parent._data.keys()):
#use the baseline start/stop values and create a sequence from start to stop
strt, stp = parent._data['baseline'][ring_cur_signame][uid]['data']
sr_data = np.linspace(strt, stp, ttlpnts, endpoint=True, dtype=np.float32)
else:
sr_data = np.array(parent._data['baseline'][ring_cur_signame][uid]['data'], dtype=np.float32)
if (resize_data):
sr_data = np.resize(sr_data, (ttlpnts,))
_dataset(nxgrp, 'data', np.reshape(sr_data, (xnpoints, num_ev_points)), 'NX_NUMBER')
_string_attr(nxgrp, 'axes', ['line_position', 'energy'])
def modify_spectra_nxdata_group(parent, data_nxgrp, doc, prim_data_arr,
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])
# x_posnr_src = rois[SPDB_X]['SRC']
y_src = parent.get_devname(rois[SPDB_Y][POSITIONER])
y_posnr_nm = parent.fix_posner_nm(rois[SPDB_Y][POSITIONER])
# y_posnr_src = rois[SPDB_Y]['SRC']
xnpoints = rois[SPDB_X][NPOINTS]
ynpoints = rois[SPDB_Y][NPOINTS]
ttlpnts = xnpoints * ynpoints
#prim_data_lst = parent._data['primary'][x_src]['data']
#uid = list(parent._cur_scan_md.keys())[0]
uid = parent.get_current_uid()
primary_det_nm = parent.get_primary_det_nm(uid)
#prim_data_lst = parent._data['primary'][primary_det_nm]['data']
#prim_data_arr = np.array(parent._data['primary'][primary_det_nm][uid]['data'])
rows = 1
cols, = prim_data_arr.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 = np.array(rois[SPDB_X][SETPOINTS], dtype=np.float32)
ydata = np.array(rois[SPDB_Y][SETPOINTS], dtype=np.float32)
else:
# use actual data
# xdata is teh first xnpoints
xdata = np.array(
parent._data['primary'][x_src][uid]['data'][0:xnpoints],
dtype=np.float32)
# ydata is every ynpoint
ydata = np.array(
parent._data['primary'][y_src][uid]['data'][0::ynpoints],
dtype=np.float32)
#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')
