add gpsans and vtk (c0482e84) · Commits · NDIP / Playground

trame/air-sans/air_sans/app/core.py

+46 −82

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@ import logging
		from trame.app import get_server
		from trame.decorators import TrameApp, change
		from trame.ui.vuetify import SinglePageWithDrawerLayout
		from trame.widgets import vuetify, plotly
		from trame.widgets import vuetify, vtk

		from .ui import (
		DeviceSelector,
		@@ -125,10 +125,22 @@ class AirSans:
		fluid=True,
		classes="pa-0 fill-height",
		):
		self.ctrl.update_d11 = plotly.Figure(
		display_mode_bar=("false",),
		v_show=("figure_ready", False),
		).update
		with vuetify.VRow(classes="fill-height pa-0"):
		with vuetify.VCol(cols=3, classes="pa-0"):
		view = vtk.VtkRemoteView(
		self._viz.left_render_window, interactive_ratio=1
		)
		self._viz.set_left_view(view)
		with vuetify.VCol(cols=6, classes="pa-0"):
		view = vtk.VtkRemoteView(
		self._viz.center_render_window, interactive_ratio=1
		)
		self._viz.set_center_view(view)
		with vuetify.VCol(cols=3, classes="pa-0"):
		view = vtk.VtkRemoteView(
		self._viz.right_render_window, interactive_ratio=1
		)
		self._viz.set_right_view(view)

		return layout

		@@ -162,92 +174,44 @@ class AirSans:
		state.file = file
		data = galaxy.load_mantid(state.file)

		# pixel_y = data["/entry0/D11/Detector 1/pixel_size_y"].nxdata[0].item()
		# pixel_x = data["/entry0/D11/Detector 1/pixel_size_x"].nxdata[0].item()
		# state.pixel_ratio = pixel_y / pixel_x
		# detector1 = data["/entry0/D11/Detector 1/data"]
		# detector1_2d = detector1[:, :, 0]
		ny, nx = data.shape
		state.pixel_ratio = 1
		state.center_ny = ny
		state.center_nx = nx
		# d1 = numpy.zeros(detector1_2d.shape, dtype=numpy.int32, order="C")
		# for i in range(0, nx - 1):
		# for j in range(0, ny - 1):
		# d1[j, i] = detector1_2d[j, i]
		#self._viz.set_center_data(d1.transpose())
		self._viz.set_center_data(data.transpose())

		# detector2 = data["/entry0/D11/Detector 2/data"]
		# detector2_2d = detector2[:, :, 0]
		# ny, nx = detector2_2d.shape
		# state.left_ny = ny
		# state.left_nx = nx
		# d2 = numpy.zeros(detector2_2d.shape, dtype=numpy.int32, order="C")
		# for i in range(0, nx - 1):
		# for j in range(0, ny - 1):
		# d2[j, i] = detector2_2d[j, i]
		# self._viz.set_left_data(d2.transpose())
		#
		# detector3 = data["/entry0/D11/Detector 3/data"]
		# detector3_2d = detector3[:, :, 0]
		# ny, nx = detector3_2d.shape
		# state.right_ny = ny
		# state.right_nx = nx
		# d3 = numpy.zeros(detector3_2d.shape, dtype=numpy.int32, order="C")
		# for i in range(0, nx - 1):
		# for j in range(0, ny - 1):
		# d3[j, i] = detector3_2d[j, i]
		# self._viz.set_right_data(d3.transpose())

		self._viz.create_gpsans_fig()
		self._viz.set_center_data(data.transpose(),1,1)
		state.figure_ready = True

		def selected_file_d11(self, file):
		state = self.server.state
		state.file = file
		data = galaxy.load(state.file)
		pixel_y = 1.0
		pixel_x = 1.0
		# print(pixel_y / pixel_x, pixel_x, type(pixel_x), pixel_y, type(pixel_y))
		pixel_y = data["/entry0/D11/Detector 1/pixel_size_y"].nxdata[0].item()
		pixel_x = data["/entry0/D11/Detector 1/pixel_size_x"].nxdata[0].item()
		# print(pixel_y / pixel_x, pixel_x, type(pixel_x), pixel_y, type(pixel_y))
		self._selected_device.read_file(self._active_directory, state.file)
		pixel_x = self._selected_device.pixel1_x
		pixel_y = self._selected_device.pixel1_y
		state.pixel_ratio = pixel_y / pixel_x
		# print(state.pixel_ratio)

		detector1 = data["/entry0/D11/Detector 1/data"]
		detector1_2d = detector1[:, :, 0]
		ny, nx = detector1_2d.shape
		state.center_ny = ny
		state.center_nx = nx
		d1 = numpy.zeros(detector1_2d.shape, dtype=numpy.int32, order="C")
		for i in range(0, nx - 1):
		for j in range(0, ny - 1):
		d1[j, i] = detector1_2d[j, i]
		self._viz.set_center_data(d1.transpose())

		detector2 = data["/entry0/D11/Detector 2/data"]
		detector2_2d = detector2[:, :, 0]
		ny, nx = detector2_2d.shape
		state.left_ny = ny
		state.left_nx = nx
		d2 = numpy.zeros(detector2_2d.shape, dtype=numpy.int32, order="C")
		for i in range(0, nx - 1):
		for j in range(0, ny - 1):
		d2[j, i] = detector2_2d[j, i]
		self._viz.set_left_data(d2.transpose())

		detector3 = data["/entry0/D11/Detector 3/data"]
		detector3_2d = detector3[:, :, 0]
		ny, nx = detector3_2d.shape
		state.right_ny = ny
		state.right_nx = nx
		d3 = numpy.zeros(detector3_2d.shape, dtype=numpy.int32, order="C")
		for i in range(0, nx - 1):
		for j in range(0, ny - 1):
		d3[j, i] = detector3_2d[j, i]
		self._viz.set_right_data(d3.transpose())
		state.center_ny = self._selected_device.ny1
		state.center_nx = self._selected_device.nx1
		self._viz.set_center_data(
		self._selected_device.det1_data,
		self._selected_device.pixel1_x,
		self._selected_device.pixel1_y,
		)

		state.left_ny = self._selected_device.ny2
		state.left_nx = self._selected_device.nx2
		self._viz.set_left_data(
		self._selected_device.det2_data,
		self._selected_device.pixel2_x,
		self._selected_device.pixel2_y,
		)

		state.right_ny = self._selected_device.ny3
		state.right_nx = self._selected_device.nx3
		self._viz.set_right_data(
		self._selected_device.det3_data,
		self._selected_device.pixel3_x,
		self._selected_device.pixel3_y,
		)

		self._viz.create_d11_fig()
		state.figure_ready = True

trame/air-sans/air_sans/app/instrument/d11_plus.py

+372 −0

Original line number	Diff line number	Diff line
		import numpy as np

		import nexusformat.nexus as nexus

		from pathlib import Path
		from . import mat_files as mf
		from ..utilities import galaxy

		BASE = Path(__file__).parent

		@@ -94,3 +97,372 @@ class D11_Plus:
		self.detector3_efficiency_error = mf.read_efficiency_mat_file_error(
		BASE / "det_efficiency" / "det3_d11_plus.mat"
		)

		def read_file(self, dir, path):
		# self.path = dir + "/" + path
		# root = nexus.nxload(self.path)
		root = galaxy.load(path)
		entry = root.NXentry[0].nxpath
		if entry is None:
		print("Bad file")
		return
		else:
		self.read_parameters(root, entry)

		def read_parameters(self, root, entry):
		# Run
		self.run_number = self.read_value(root, entry, "/run_number")
		self.user = self.read_value(root, entry, "/user/name")
		self.start_time = self.read_value(root, entry, "/start_time")
		self.end_time = self.read_value(root, entry, "/end_time")
		self.duration = self.read_value(root, entry, "/duration")
		self.experiment_identifier = self.read_value(
		root, entry, "/experiment_identifier"
		)
		self.experiment_title = self.read_value(root, entry, "/experiment_title")
		self.sample_description = self.read_value(root, entry, "/sample_description")

		# Detector Distance & Motors
		self.pixel1_y = self.read_value(root, entry, "/D11/Detector 1/pixel_size_y")
		self.pixel1_x = self.read_value(root, entry, "/D11/Detector 1/pixel_size_x")
		# Detector rate
		self.det1_rate = self.read_value(root, entry, "/D11/Detector 1/det1_rate")
		# Detector motors
		self.det1_actual = self.read_value(root, entry, "/D11/Detector 1/det1_actual")
		if self.det1_actual is None:
		self.det1_actual = self.read_value(
		root, entry, "/D11/Detector 1/det_actual"
		)
		self.det1_calc = self.read_value(root, entry, "/D11/Detector 1/det1_calc")
		if self.det1_calc is None:
		self.det1_calc = self.read_value(root, entry, "/D11/Detector 1/det_calc")
		self.dan1_actual = self.read_value(root, entry, "/D11/Detector 1/dan1_actual")
		if self.dan1_actual is None:
		self.dan1_actual = self.read_value(
		root, entry, "/D11/Detector 1/dan_actual"
		)
		self.dtr1_actual = self.read_value(root, entry, "/D11/Detector 1/dtr1_actual")
		if self.dtr1_actual is None:
		self.dtr1_actual = self.read_value(
		root, entry, "/D11/Detector 1/dtr_actual"
		)
		# BeamStop
		self.bx1_actual = self.read_value(root, entry, "/D11//beamstop/bx1_actual")
		if self.bx1_actual is None:
		self.bx1_actual = self.read_value(root, entry, "/D11//beamstop/bx_actual")
		if self.bx1_actual is None:
		self.bx1_actual = 0.0
		print("/D11//beamstop/bx1_actual", self.bx1_actual)
		self.by1_actual = self.read_value(root, entry, "/D11//beamstop/by1_actual")
		if self.by1_actual is None:
		self.by1_actual = self.read_value(root, entry, "/D11//beamstop/by_actual")
		if self.by1_actual is None:
		self.by1_actual = 0.0
		print("/D11//beamstop/by1_actual", self.by1_actual)

		self.pixel2_y = self.read_value(root, entry, "/D11/Detector 2/pixel_size_y")
		self.pixel2_x = self.read_value(root, entry, "/D11/Detector 2/pixel_size_x")
		# Detector rate
		self.det2_rate = self.read_value(root, entry, "/D11/Detector 2/det2_rate")
		# Detector motors
		self.det2_actual = self.read_value(root, entry, "/D11/Detector 2/det2_actual")
		if self.det2_actual is None:
		self.det2_actual = self.read_value(
		root, entry, "/D11/Detector 2/det_actual"
		)
		self.det2_calc = self.read_value(root, entry, "/D11/Detector 2/det2_calc")
		if self.det2_calc is None:
		self.det2_calc = self.read_value(root, entry, "/D11/Detector 2/det_calc")
		self.dan2_actual = self.read_value(root, entry, "/D11/Detector 2/dan2_actual")
		if self.dan2_actual is None:
		self.dan2_actual = self.read_value(
		root, entry, "/D11/Detector 2/dan_actual"
		)
		self.dtr2_actual = self.read_value(root, entry, "/D11/Detector 2/dtr2_actual")
		if self.dtr2_actual is None:
		self.dtr2_actual = self.read_value(
		root, entry, "/D11/Detector 2/dtr_actual"
		)
		# BeamStop
		self.bx2_actual = self.read_value(root, entry, "/D11//beamstop/bx2_actual")
		if self.bx2_actual is None:
		self.bx2_actual = self.read_value(root, entry, "/D11//beamstop/bx_actual")
		if self.bx2_actual is None:
		self.bx2_actual = 0.0
		print("/D11//beamstop/bx2_actual", self.bx2_actual)
		self.by2_actual = self.read_value(root, entry, "/D11//beamstop/by2_actual")
		if self.by2_actual is None:
		self.by2_actual = self.read_value(root, entry, "/D11//beamstop/by_actual")
		if self.by2_actual is None:
		self.by2_actual = 0.0
		print("/D11//beamstop/by2_actual", self.by2_actual)

		self.pixel3_y = self.read_value(root, entry, "/D11/Detector 3/pixel_size_y")
		self.pixel3_x = self.read_value(root, entry, "/D11/Detector 3/pixel_size_x")
		# Detector rate
		self.det3_rate = self.read_value(root, entry, "/D11/Detector 3/det3_rate")
		# Detector motors
		self.det3_actual = self.read_value(root, entry, "/D11/Detector 3/det3_actual")
		if self.det3_actual is None:
		self.det3_actual = self.read_value(
		root, entry, "/D11/Detector 3/det_actual"
		)
		self.det3_calc = self.read_value(root, entry, "/D11/Detector 3/det3_calc")
		if self.det3_calc is None:
		self.det3_calc = self.read_value(root, entry, "/D11/Detector 3/det_calc")
		self.dan3_actual = self.read_value(root, entry, "/D11/Detector 3/dan3_actual")
		if self.dan3_actual is None:
		self.dan3_actual = self.read_value(
		root, entry, "/D11/Detector 3/dan_actual"
		)
		self.dtr3_actual = self.read_value(root, entry, "/D11/Detector 3/dtr3_actual")
		if self.dtr3_actual is None:
		self.dtr3_actual = self.read_value(
		root, entry, "/D11/Detector 3/dtr_actual"
		)
		# BeamStop
		self.bx3_actual = self.read_value(root, entry, "/D11//beamstop/bx3_actual")
		self.bx3_actual = self.read_value(root, entry, "/D11//beamstop/bx3_actual")
		if self.bx3_actual is None:
		self.bx3_actual = self.read_value(root, entry, "/D11//beamstop/bx_actual")
		if self.bx3_actual is None:
		self.bx3_actual = 0.0
		print("/D11//beamstop/bx3_actual", self.bx3_actual)
		self.by3_actual = self.read_value(root, entry, "/D11//beamstop/by3_actual")
		if self.by3_actual is None:
		self.by3_actual = self.read_value(root, entry, "/D11//beamstop/by_actual")
		if self.by3_actual is None:
		self.by3_actual = 0.0
		print("/D11//beamstop/by3_actual", self.by3_actual)

		# Wavelength
		self.wavelength = self.read_value(root, entry, "/D11/selector/wavelength")
		self.wavelength_res = (
		self.read_value(root, entry, "/D11/selector/wavelength_res") / 100
		)
		if self.wavelength_res is None:
		self.wavelength_res = 0.1
		self.rotation_speed = self.read_value(
		root, entry, "/D11/selector/rotation_speed"
		)
		self.seltrs_actual = self.read_value(root, entry, "/D11/selector/seltrs_actual")

		# Attenuator
		self.attenuator_position = self.read_value(
		root, entry, "/D11/attenuator/position"
		)
		if self.attenuator_position is None:
		self.attenuator_position = 0
		self.attenuation_coefficient = self.read_value(
		root, entry, "/D11/attenuator/attenuation_coefficient"
		)
		self.attenuation_value = self.read_value(
		root, entry, "/D11/attenuator/attenuation_value"
		)
		if self.attenuation_value is None:
		self.attenuation_value = [
		self.attenuators[1],
		self.attenuators[2],
		self.attenuators[3],
		]
		print("/D11/attenuator/attenuation_value", self.attenuation_value)

		# Collimation
		self.collimation_actual_position = self.read_value(
		root, entry, "/D11/collimation/actual_position"
		)
		# Source Size
		temp = self.read_value(root, entry, "/D11/collimation/ap_size")
		if temp is not None:
		self.collimation_ap_size_x = temp[0] / 1000
		self.collimation_ap_size_y = temp[1] / 1000
		else:
		self.collimation_ap_size_x = self.guide_size[0]
		self.collimation_ap_size_y = self.guide_size[1]
		print(
		"/D11/collimation/ap_size",
		self.collimation_ap_size_x,
		self.collimation_ap_size_y,
		)

		# Reactor Power
		self.reactor_power = self.read_value(root, entry, "/reactor_power")

		# Sample
		self.sample_thickness = self.read_value(root, entry, "/sample/thickness")

		# Sample Motors
		self.sample_san_actual = self.read_value(root, entry, "/sample/san_actual")
		self.sample_phi_actual = self.read_value(root, entry, "/sample/phi_actual")
		self.sample_sdi1_actual = self.read_value(root, entry, "/sample/sdi1_actual")
		self.sample_sdi_actual = self.read_value(root, entry, "/sample/sdi_actual")
		self.sample_sdi2_actual = self.read_value(root, entry, "/sample/sdi2_actual")
		self.sample_trs_actual = self.read_value(root, entry, "/sample/trs_actual")
		self.sample_sht_actual = self.read_value(root, entry, "/sample/sht_actual")
		self.sample_str_actual = self.read_value(root, entry, "/sample/str_actual")
		self.sample_changer_value = self.read_value(
		root, entry, "/sample/sample_changer_value"
		)
		self.sample_omega_actual = self.read_value(root, entry, "/sample/omega_actual")
		self.sample_TrMicro_actual = self.read_value(
		root, entry, "/sample/TrMicro_actual"
		)
		self.sample_TrMicro_offset = self.read_value(
		root, entry, "/sample/TrMicro_offset"
		)
		self.sample_TrMicro_requested = self.read_value(
		root, entry, "/sample/TrMicro_requested"
		)

		# Sample environment
		self.sample_temperature = self.read_value(root, entry, "/sample/temperature")
		self.sample_regulation_temperature = self.read_value(
		root, entry, "/sample/regulation_temperature"
		)
		self.sample_setpoint_temperature = self.read_value(
		root, entry, "/sample/setpoint_temperature"
		)
		self.sample_bath1_regulation_temperature = self.read_value(
		root, entry, "/sample/bath1_regulation_temperature"
		)
		self.sample_bath1_setpoint_temperature = self.read_value(
		root, entry, "/sample/bath1_setpoint_temperature"
		)
		self.sample_bath2_regulation_temperature = self.read_value(
		root, entry, "/sample/bath2_regulation_temperature"
		)
		self.sample_bath2_setpoint_temperature = self.read_value(
		root, entry, "/sample/bath2_setpoint_temperature"
		)
		self.sample_bath_selector_actual = self.read_value(
		root, entry, "/sample/bath_selector_actual"
		)
		self.sample_air_temperature = self.read_value(
		root, entry, "/sample/air_temperature"
		)
		self.sample_rack_temperature = self.read_value(
		root, entry, "/sample/rack_temperature"
		)

		# Power Supplies
		self.sample_ps1_current = self.read_value(root, entry, "/sample/ps1_current")
		self.sample_ps1_voltage = self.read_value(root, entry, "/sample/ps1_voltage")
		self.sample_ps2_current = self.read_value(root, entry, "/sample/ps2_current")
		self.sample_ps2_voltage = self.read_value(root, entry, "/sample/ps2_voltage")
		self.sample_ps3_current = self.read_value(root, entry, "/sample/ps3_current")
		self.sample_ps3_voltage = self.read_value(root, entry, "/sample/ps3_voltage")

		# Magnet
		self.sample_field_actual = self.read_value(root, entry, "/sample/field_actual")

		# Shear
		self.sample_shearrate_actual = self.read_value(
		root, entry, "/sample/shearrate_actual"
		)

		# Read Detector Data, Monitor and Time Slices
		self.detector_detsum = self.read_value(root, entry, "/detector/detsum")
		self.detector_detrate = self.read_value(root, entry, "/detector/detrate")

		# Determine Measurement Mode, Single, Kinetic or TOF
		self.mode = self.read_value(root, entry, "/mode")
		if temp is not None:
		self.mode = int(temp)
		else:
		self.mode = 0
		if self.mode == 0:
		self.file_type = "mono"
		elif self.mode == 1:
		self.file_type = "tof"
		tof_params = self.read_value(root, entry, "/monitor1/time_of_flight")
		if tof_params is not None:
		self.tof_width = tof_params[0]
		self.tof_channels = tof_params[1]
		self.tof_delay = tof_params[2]
		self.pickups = self.read_value(root, entry, "/monitor1/nbpickup")
		self.tof_period = (self.tof_width * self.tof_channels) + self.tof_delay
		self.tof_mode = self.read_value(root, entry, "/tof/tof_mode")
		if self.tof_mode is None:
		self.tof_mode = 0
		elif self.mode == 22:
		self.file_type = "tof"
		tof_params = self.read_value(root, entry, "/monitor1/time_of_flight")
		if tof_params is not None:
		self.tof_width = tof_params[0]
		self.tof_channels = tof_params[1]
		self.tof_delay = tof_params[2]
		self.pickups = self.read_value(root, entry, "/monitor1/nbpickup")
		self.tof_period = (self.tof_width * self.tof_channels) + self.tof_delay
		self.tof_mode = self.read_value(root, entry, "/tof/tof_mode")
		if self.tof_mode is None:
		self.tof_mode = 0
		elif self.mode == 3:
		self.file_type = "kinetic"
		self.slices = self.read_value(root, entry, "/slices")
		if self.slices is not None:
		# time lapse of the first frame - added to below with subsequent frames
		self.frame_time = self.slices[0] / 2
		self.pickups = self.read_value(root, entry, "/nbrepaint")
		elif self.mode == 4:
		self.file_type = "tof_inelastic"
		tof_params = self.read_value(root, entry, "/monitor1/time_of_flight")
		if tof_params is not None:
		self.tof_width = tof_params[0]
		self.tof_channels = tof_params[1]
		self.tof_delay = tof_params[2]
		self.pickups = self.read_value(root, entry, "/monitor1/nbpickup")
		self.tof_period = (self.tof_width * self.tof_channels) + self.tof_delay
		else:
		self.file_type = "unknown"

		# Detector Distance & Motors

		det = self.read_array(
		root, entry, "/D11/Detector 1/data1", "/D11/Detector 1/data"
		)
		det_size = det.shape
		if len(det_size) < 3:
		det_size[2] = 1
		if self.file_type == "mono":
		det = det.reshape([det_size[2], det_size[0], det_size[1]])
		self.n_frames = det_size[2]
		self.det1_data = det[0, :, :].nxvalue.transpose()
		self.nx1, self.ny1 = self.det1_data.shape
		det = self.read_array(
		root, entry, "/D11/Detector 2/data2", "/D11/Detector 2/data"
		)
		det_size = det.shape
		if len(det_size) < 3:
		det_size[2] = 1
		if self.file_type == "mono":
		det = det.reshape([det_size[2], det_size[0], det_size[1]])
		self.det2_data = det[0, :, :].nxvalue.transpose()
		self.nx2, self.ny2 = self.det2_data.shape
		det = self.read_array(
		root, entry, "/D11/Detector 3/data3", "/D11/Detector 3/data"
		)
		det_size = det.shape
		if len(det_size) < 3:
		det_size[2] = 1
		if self.file_type == "mono":
		det = det.reshape([det_size[2], det_size[0], det_size[1]])
		self.det3_data = det[0, :, :].nxvalue.transpose()
		self.nx3, self.ny3 = self.det3_data.shape

		def read_value(self, root, entry, item):
		try:
		value = root[entry + item]
		except Exception:
		return None
		return value.nxdata[0].item()

		def read_array(self, root, entry, item, fallback_item):
		try:
		value = root[entry + item]
		except Exception:
		try:
		value = root[entry + fallback_item]
		except Exception:
		print("Bad file")
		return None
		return value

trame/air-sans/air_sans/app/visualization.py

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trame/air-sans/air_sans/app/vtk.py

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