Synchrotrons¶
Here we report the meta data generated by tomography instruments installed at different synchrotron facilities.
APS¶
At the Advanced Photon Source (APS) experimental meta-data are stored in the HDF file together with the raw data.
A meta-data reader is available at hdf reder
Meta-data are saved automatically for each scan by reading the beamline configuration (motor positions) of all beamline components, this includes lens, scintillator, energy, sample to detector distance, etc. Other parameters, like user and proposal information, are collected by automatically accessing the APS user proposal data base. Tomography scan parameters are automatically added by the tomoScan engine.
The full and up-to-date list of meta-data stored at the APS tomography beamlines is available at DXfile. A python script to extract as a text file the APS meta-data from the raw data HDF file is available at meta cli.
The APS meta-data also include all parameters required to complete a tomographic reconstruction including sample to detector distance, x-ray energy, pixel size, etc.; these parameters are extracted automatically and used by the beamline reconstruction software tomoPy and tomocuPy .
Additionally, when using tomopy cli, all reconstruction parameters like the center of rotation, the ring removal filter used as well as the version of the software used are stored in the HDF file. This guarantees full data collection and data analysis pipe-line repeatability.
Beamline 2-BM μCT¶
The full and up-to-date list of meta-data stored at the APS beamline 2-BM is available at DXfile. A meta-data reader is available at hdf reder
APS 2-BM Scalar meta data¶
Meta data name |
Value |
Units |
/measurement/instrument/attenuator/name |
2-BM-A user filters |
|
/measurement/instrument/attenuator/setup/down_stream |
0 |
|
/measurement/instrument/attenuator/setup/down_stream_list |
0:600um Al; 1: 50um Al; 2:300um C; 3:50um C; 4:None; 5:LowLimit |
|
/measurement/instrument/attenuator/setup/up_stream |
0 |
|
/measurement/instrument/attenuator/setup/up_stream_list |
0:1mm C; 1:150um Al; 2:600um Al; 3:1mm Al; 4:None; 5:LowLimit |
|
/measurement/instrument/attenuator_1/description |
||
/measurement/instrument/attenuator_1/name |
Manually added filters |
|
/measurement/instrument/detection_system/objective/magnification |
2.0 |
|
/measurement/instrument/detection_system/objective/resolution |
1.725 |
μm |
/measurement/instrument/detection_system/objective/tube_length |
1.0 |
mm |
/measurement/instrument/detection_system/scintillator/active_thickness |
50.0 |
μm |
/measurement/instrument/detection_system/scintillator/type |
LuAG |
|
/measurement/instrument/detector/acquire_period |
0.030257840000000005 |
s |
/measurement/instrument/detector/adcore_version |
3.12.1 |
|
/measurement/instrument/detector/array_counter |
311623 |
|
/measurement/instrument/detector/array_size_x |
3464 |
pixel |
/measurement/instrument/detector/array_size_y |
2652 |
pixel |
/measurement/instrument/detector/binning_x |
1 |
|
/measurement/instrument/detector/binning_y |
1 |
|
/measurement/instrument/detector/convert_pixel_format |
Mono16 |
|
/measurement/instrument/detector/data_type |
UInt16 |
|
/measurement/instrument/detector/driver_version |
3.3.0 |
|
/measurement/instrument/detector/exposure_auto |
0 |
|
/measurement/instrument/detector/exposure_time |
0.100001 |
s |
/measurement/instrument/detector/firmware_version |
1904.0.72.0 |
|
/measurement/instrument/detector/frame_rate |
33.04928573883661 fps |
|
/measurement/instrument/detector/frame_rate_enable |
No |
|
/measurement/instrument/detector/gain |
0.9998811256880493 |
|
/measurement/instrument/detector/gain_auto |
0 |
|
/measurement/instrument/detector/hdf_plugin_version |
NDFileHDF5 ver1.10.1 |
|
/measurement/instrument/detector/manufacturer |
FLIR |
|
/measurement/instrument/detector/max_size_x |
6464 |
pixel |
/measurement/instrument/detector/max_size_y |
4852 |
pixel |
/measurement/instrument/detector/model |
Oryx ORX-10G-310S9M |
|
/measurement/instrument/detector/pixel_format |
Mono16 |
|
/measurement/instrument/detector/pixel_size |
3.45 |
μm |
/measurement/instrument/detector/roi/min_x |
1496 |
pixel |
/measurement/instrument/detector/roi/min_y |
1000 |
pixel |
/measurement/instrument/detector/roi/size_x |
3464 |
pixel |
/measurement/instrument/detector/roi/size_y |
2652 |
pixel |
/measurement/instrument/detector/sdk_version |
2.4.0.143 |
|
/measurement/instrument/detector/serial_number |
22150530 |
|
/measurement/instrument/detector/temperature |
44.625 |
°C |
/measurement/instrument/detector_motor_stack/name |
2-BM-A detector motor stack |
|
/measurement/instrument/detector_motor_stack/setup/roll |
0.7300625 |
° |
/measurement/instrument/detector_motor_stack/setup/z |
50.0 |
mm |
/measurement/instrument/mirror/name |
2-BM Mirror |
|
/measurement/instrument/mirror/setup/angle |
2.657051349174385 |
mrad |
/measurement/instrument/mirror/setup/dsy |
1.5195162 |
mm |
/measurement/instrument/mirror/setup/stripe |
1 |
|
/measurement/instrument/mirror/setup/stripe_legend |
0:Cr; 1:Pt |
|
/measurement/instrument/mirror/setup/usy |
-1.119467199999999 |
mm |
/measurement/instrument/mirror/setup/x |
-17.000225 |
mm |
/measurement/instrument/mirror/setup/y |
0.2000245000000005 |
mm |
/measurement/instrument/monochromator/energy |
25.51 |
keV |
/measurement/instrument/monochromator/mode |
0 |
|
/measurement/instrument/monochromator/mode_legend |
0:mono; 1:pink; 2:white |
|
/measurement/instrument/monochromator/name |
2-BM-A double multilayer monochromator |
|
/measurement/instrument/monochromator/setup/ds_arm |
1.1400979000000007 |
° |
/measurement/instrument/monochromator/setup/m2_y |
12.350145000000001 |
mm |
/measurement/instrument/monochromator/setup/m2_z |
600.00011 |
mm |
/measurement/instrument/monochromator/setup/table_ds_y |
-0.10046250000000256 |
mm |
/measurement/instrument/monochromator/setup/table_usy_ib |
-0.10050000000000026 |
mm |
/measurement/instrument/monochromator/setup/table_usy_ob |
-0.1004875000000034 |
mm |
/measurement/instrument/monochromator/setup/us_arm |
1.06515328101057 |
° |
/measurement/instrument/name |
Micro-tomography |
|
/measurement/instrument/sample_motor_stack/name |
microCT sample stage stack |
|
/measurement/instrument/sample_motor_stack/setup/pitch |
0.0 |
° |
/measurement/instrument/sample_motor_stack/setup/roll |
-0.019999999999999907 |
° |
/measurement/instrument/sample_motor_stack/setup/rotary |
180.012 |
° |
/measurement/instrument/sample_motor_stack/setup/top/x |
1.01 |
mm |
/measurement/instrument/sample_motor_stack/setup/top/z |
-1.200000482 |
mm |
/measurement/instrument/sample_motor_stack/setup/x |
6.927791673660977e-14 |
mm |
/measurement/instrument/sample_motor_stack/setup/y |
5.4999999999999964 |
mm |
/measurement/instrument/slits/downstream/horizontal/setup/center |
-0.050000000000000044 |
mm |
/measurement/instrument/slits/downstream/horizontal/setup/size |
7.1 |
mm |
/measurement/instrument/slits/downstream/vertical/setup/center |
15.199999999999966 |
mm |
/measurement/instrument/slits/downstream/vertical/setup/size |
3.8000000000000007 |
mm |
/measurement/instrument/slits/name |
2-BM slits |
|
/measurement/instrument/slits/upstream/horizontal/setup/center |
0.2093999999999987 |
mm |
/measurement/instrument/slits/upstream/horizontal/setup/size |
14.0 |
mm |
/measurement/instrument/slits/upstream/vertical/setup/center |
0.15559999999999974 |
mm |
/measurement/instrument/slits/upstream/vertical/setup/size |
8.6584 |
mm |
/measurement/instrument/source/beamline |
2-BM |
|
/measurement/instrument/source/current |
102.05313028920399 |
mA |
/measurement/instrument/source/fill_mode |
0+24x1 |
|
/measurement/instrument/source/name |
Advanced Photon Source |
|
/measurement/instrument/source/top_up |
Enable |
|
/measurement/sample/description_1 |
||
/measurement/sample/description_2 |
||
/measurement/sample/description_3 |
||
/measurement/sample/environment/eurotherm1/d |
nan |
|
/measurement/sample/environment/eurotherm1/i |
nan |
|
/measurement/sample/environment/eurotherm1/p |
nan |
|
/measurement/sample/environment/eurotherm1/pid_mode |
nan |
|
/measurement/sample/environment/eurotherm1/pid_update_rate |
nan |
s |
/measurement/sample/environment/eurotherm1/ramp_rate |
nan |
°C/s |
/measurement/sample/environment/eurotherm1/set_point |
nan |
°C |
/measurement/sample/environment/eurotherm1/status |
nan |
|
/measurement/sample/environment/eurotherm1/thermocouple |
nan |
°C |
/measurement/sample/environment/eurotherm1/update_rate |
nan |
s |
/measurement/sample/environment/eurotherm2/d |
nan |
|
/measurement/sample/environment/eurotherm2/i |
nan |
|
/measurement/sample/environment/eurotherm2/p |
nan |
|
/measurement/sample/environment/eurotherm2/pid_mode |
nan |
|
/measurement/sample/environment/eurotherm2/pid_update_rate |
nan |
s |
/measurement/sample/environment/eurotherm2/ramp_rate |
nan |
°C/s |
/measurement/sample/environment/eurotherm2/set_point |
nan |
°C |
/measurement/sample/environment/eurotherm2/status |
nan |
|
/measurement/sample/environment/eurotherm2/thermocouple |
nan |
°C |
/measurement/sample/environment/eurotherm2/update_rate |
nan |
s |
/measurement/sample/environment/load_cell/load_calc |
48.9485636115582 |
N |
/measurement/sample/environment/load_cell/load_raw |
-0.0477383047 |
V |
/measurement/sample/experiment/proposal |
74328 |
|
/measurement/sample/experiment/safety_id |
||
/measurement/sample/experiment/title |
Studying the role of fluoride in the formation of early-stage caries |
|
/measurement/sample/experimenter/email |
||
/measurement/sample/experimenter/institution |
Northwesteversity |
|
/measurement/sample/experimenter/name |
Boyer |
|
/measurement/sample/experimenter/user_id |
313356 |
|
/measurement/sample/file/full_name |
/local/data/2023-02/Boyer/295_2RMAN_089.h5 |
|
/measurement/sample/file/name 295_2RMAN |
||
/measurement/sample/file/path |
/local/data/2023-02/Boyer/ |
|
/measurement/sample/name |
||
/process/acquisition/dark_fields/mode |
Start |
|
/process/acquisition/dark_fields/number |
20 |
|
/process/acquisition/dark_fields/value |
0.0 |
counts |
/process/acquisition/end_date |
2023-02-10T08:49:14-0600 |
|
/process/acquisition/flat_fields/axis |
X |
|
/process/acquisition/flat_fields/different_flat_exposure |
Same |
|
/process/acquisition/flat_fields/flat_exposure_time |
0.08 |
s |
/process/acquisition/flat_fields/mode |
Start |
|
/process/acquisition/flat_fields/number |
20 |
|
/process/acquisition/flat_fields/sample/in_x |
0.0 |
mm |
/process/acquisition/flat_fields/sample/in_y |
13.1 |
mm |
/process/acquisition/flat_fields/sample/out_x |
11.0 |
mm |
/process/acquisition/flat_fields/sample/out_y |
1.0 |
mm |
/process/acquisition/flat_fields/sample_out_angle |
0.000 |
|
/process/acquisition/flat_fields/sample_out_angle_enable |
No |
|
/process/acquisition/flat_fields/value |
0.0 |
counts |
/process/acquisition/flip_stitch |
No |
|
/process/acquisition/rotation/num_angles |
2001 |
|
/process/acquisition/rotation/return |
Yes |
|
/process/acquisition/rotation/speed |
0.8181736364454536 |
°/s |
/process/acquisition/rotation/start |
0.0 |
° |
/process/acquisition/rotation/step |
0.09 |
° |
/process/acquisition/scan_type |
Single |
|
/process/acquisition/start_date |
2023-02-10T08:45:01-0600 |
APS 2-BM Full layout¶
├── defaults
│ │
│ ├── ColorMode (2041,)
│ ├── HDF5FrameLocation (2041,)
│ ├── NDArrayEpicsTSSec (2041,)
│ ├── NDArrayEpicsTSnSec (2041,)
│ ├── NDArrayTimeStamp (2041,)
│ ├── NDArrayUniqueId (2041,)
│ └── timestamp (2041, 5)
├── exchange
│ │
│ ├── data (2001, 2652, 3464)
│ ├── data_dark (20, 2652, 3464)
│ ├── data_white (20, 2652, 3464)
│ ├── theta (2001,)
│ └── web_camera_frame (360, 640, 3)
├── measurement
│ │
│ ├── instrument
│ │ │
│ │ ├── attenuator
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── down_stream (1,)
│ │ │ ├── down_stream_list (1,)
│ │ │ ├── up_stream (1,)
│ │ │ └── up_stream_list (1,)
│ │ ├── attenuator_1
│ │ │ │
│ │ │ ├── description (1,)
│ │ │ └── name (1,)
│ │ ├── detection_system
│ │ │ │
│ │ │ ├── objective
│ │ │ │ │
│ │ │ │ ├── magnification (1,)
│ │ │ │ ├── resolution (1,)
│ │ │ │ └── tube_length (1,)
│ │ │ └── scintillator
│ │ │ │
│ │ │ ├── active_thickness (1,)
│ │ │ └── type (1,)
│ │ ├── detector
│ │ │ │
│ │ │ ├── acquire_period (1,)
│ │ │ ├── adcore_version (1,)
│ │ │ ├── array_counter (1,)
│ │ │ ├── array_size_x (1,)
│ │ │ ├── array_size_y (1,)
│ │ │ ├── binning_x (1,)
│ │ │ ├── binning_y (1,)
│ │ │ ├── convert_pixel_format (1,)
│ │ │ ├── data_type (1,)
│ │ │ ├── driver_version (1,)
│ │ │ ├── exposure_auto (1,)
│ │ │ ├── exposure_time (1,)
│ │ │ ├── firmware_version (1,)
│ │ │ ├── frame_rate (1,)
│ │ │ ├── frame_rate_enable (1,)
│ │ │ ├── gain (1,)
│ │ │ ├── gain_auto (1,)
│ │ │ ├── hdf_plugin_version (1,)
│ │ │ ├── manufacturer (1,)
│ │ │ ├── max_size_x (1,)
│ │ │ ├── max_size_y (1,)
│ │ │ ├── model (1,)
│ │ │ ├── pixel_format (1,)
│ │ │ ├── pixel_size (1,)
│ │ │ ├── roi
│ │ │ │ │
│ │ │ │ ├── min_x (1,)
│ │ │ │ ├── min_y (1,)
│ │ │ │ ├── size_x (1,)
│ │ │ │ └── size_y (1,)
│ │ │ ├── sdk_version (1,)
│ │ │ ├── serial_number (1,)
│ │ │ └── temperature (1,)
│ │ ├── detector_motor_stack
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── roll (1,)
│ │ │ └── z (1,)
│ │ ├── mirror
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── angle (1,)
│ │ │ ├── dsy (1,)
│ │ │ ├── stripe (1,)
│ │ │ ├── stripe_legend (1,)
│ │ │ ├── usy (1,)
│ │ │ ├── x (1,)
│ │ │ └── y (1,)
│ │ ├── monochromator
│ │ │ │
│ │ │ ├── energy (1,)
│ │ │ ├── mode (1,)
│ │ │ ├── mode_legend (1,)
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── ds_arm (1,)
│ │ │ ├── m2_y (1,)
│ │ │ ├── m2_z (1,)
│ │ │ ├── table_ds_y (1,)
│ │ │ ├── table_usy_ib (1,)
│ │ │ ├── table_usy_ob (1,)
│ │ │ └── us_arm (1,)
│ │ ├── name (1,)
│ │ ├── sample_motor_stack
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── pitch (1,)
│ │ │ ├── roll (1,)
│ │ │ ├── rotary (1,)
│ │ │ ├── top
│ │ │ │ │
│ │ │ │ ├── x (1,)
│ │ │ │ └── z (1,)
│ │ │ ├── x (1,)
│ │ │ └── y (1,)
│ │ ├── slits
│ │ │ │
│ │ │ ├── downstream
│ │ │ │ │
│ │ │ │ ├── horizontal
│ │ │ │ │ └── setup
│ │ │ │ │ │
│ │ │ │ │ ├── center (1,)
│ │ │ │ │ └── size (1,)
│ │ │ │ └── vertical
│ │ │ │ └── setup
│ │ │ │ │
│ │ │ │ ├── center (1,)
│ │ │ │ └── size (1,)
│ │ │ ├── name (1,)
│ │ │ └── upstream
│ │ │ │
│ │ │ ├── horizontal
│ │ │ │ └── setup
│ │ │ │ │
│ │ │ │ ├── center (1,)
│ │ │ │ └── size (1,)
│ │ │ └── vertical
│ │ │ └── setup
│ │ │ │
│ │ │ ├── center (1,)
│ │ │ └── size (1,)
│ │ └── source
│ │ │
│ │ ├── beamline (1,)
│ │ ├── current (1,)
│ │ ├── fill_mode (1,)
│ │ ├── name (1,)
│ │ └── top_up (1,)
│ └── sample
│ │
│ ├── description_1 (1,)
│ ├── description_2 (1,)
│ ├── description_3 (1,)
│ ├── environment
│ │ │
│ │ ├── eurotherm1
│ │ │ │
│ │ │ ├── d (1,)
│ │ │ ├── i (1,)
│ │ │ ├── p (1,)
│ │ │ ├── pid_mode (1,)
│ │ │ ├── pid_update_rate (1,)
│ │ │ ├── ramp_rate (1,)
│ │ │ ├── set_point (1,)
│ │ │ ├── status (1,)
│ │ │ ├── thermocouple (1,)
│ │ │ └── update_rate (1,)
│ │ ├── eurotherm2
│ │ │ │
│ │ │ ├── d (1,)
│ │ │ ├── i (1,)
│ │ │ ├── p (1,)
│ │ │ ├── pid_mode (1,)
│ │ │ ├── pid_update_rate (1,)
│ │ │ ├── ramp_rate (1,)
│ │ │ ├── set_point (1,)
│ │ │ ├── status (1,)
│ │ │ ├── thermocouple (1,)
│ │ │ └── update_rate (1,)
│ │ └── load_cell
│ │ │
│ │ ├── load_calc (1,)
│ │ └── load_raw (1,)
│ ├── experiment
│ │ │
│ │ ├── proposal (1,)
│ │ ├── safety_id (1,)
│ │ └── title (1,)
│ ├── experimenter
│ │ │
│ │ ├── email (1,)
│ │ ├── institution (1,)
│ │ ├── name (1,)
│ │ └── user_id (1,)
│ ├── file
│ │ │
│ │ ├── full_name (1,)
│ │ ├── name (1,)
│ │ └── path (1,)
│ └── name (1,)
└── process
└── acquisition
│
├── dark_fields
│ │
│ ├── mode (1,)
│ ├── number (1,)
│ └── value (1,)
├── end_date (1,)
├── flat_fields
│ │
│ ├── axis (1,)
│ ├── different_flat_exposure (1,)
│ ├── flat_exposure_time (1,)
│ ├── mode (1,)
│ ├── number (1,)
│ ├── sample
│ │ │
│ │ ├── in_x (1,)
│ │ ├── in_y (1,)
│ │ ├── out_x (1,)
│ │ └── out_y (1,)
│ ├── sample_out_angle (1,)
│ ├── sample_out_angle_enable (1,)
│ └── value (1,)
├── flip_stitch (1,)
├── rotation
│ │
│ ├── num_angles (1,)
│ ├── return (1,)
│ ├── speed (1,)
│ ├── start (1,)
│ └── step (1,)
├── scan_type (1,)
└── start_date (1,)
Beamline 7-BM μCT¶
The full and up-to-date list of meta-data stored at the APS beamline 7-BM is available at DXfile. A meta-data reader is available at hdf reder
APS 7-BM scalar meta data¶
Meta data name |
Value |
Units |
/measurement/ancillary/BarometricPressure |
986.1626095155999 |
mbar |
/measurement/instrument/attenuator_1/description |
Be |
|
/measurement/instrument/attenuator_1/name |
7-BM Be Windows |
|
/measurement/instrument/attenuator_1/thickness |
750 |
|
/measurement/instrument/attenuator_2/name |
7-BM-A Filter 1 |
|
/measurement/instrument/attenuator_2/setup/filter_unit_text |
Open |
|
/measurement/instrument/attenuator_3/name 7-BM-A Filter |
2 |
|
/measurement/instrument/attenuator_3/setup/filter_unit_text |
Cu_1000um |
|
/measurement/instrument/detection_system/objective/magnification |
5x |
|
/measurement/instrument/detection_system/objective/resolution |
1.3717421124828533 |
μm |
/measurement/instrument/detection_system/objective/tube_length |
0.0 |
mm |
/measurement/instrument/detection_system/scintillator/active_thickness |
25.0 |
μm |
/measurement/instrument/detection_system/scintillator/type |
LuAG:Ce |
|
/measurement/instrument/detector/acquire_period |
0.009966864 |
s |
/measurement/instrument/detector/adcore_version |
3.12.1 |
|
/measurement/instrument/detector/array_counter |
6266125 |
|
/measurement/instrument/detector/array_size_x |
3232 |
|
/measurement/instrument/detector/array_size_y |
1200 |
|
/measurement/instrument/detector/binning_x |
2 |
|
/measurement/instrument/detector/binning_y |
2 |
|
/measurement/instrument/detector/convert_pixel_format |
Mono16 |
|
/measurement/instrument/detector/data_type |
UInt16 |
|
/measurement/instrument/detector/driver_version |
3.3.0 |
|
/measurement/instrument/detector/exposure_auto |
0 |
|
/measurement/instrument/detector/exposure_time |
0.060003 |
s |
/measurement/instrument/detector/firmware_version |
1904.0.72.0 |
|
/measurement/instrument/detector/frame_rate |
100.33246164490656 |
fps |
/measurement/instrument/detector/frame_rate_enable |
No |
|
/measurement/instrument/detector/gain |
0.0 |
|
/measurement/instrument/detector/gain_auto |
0 |
|
/measurement/instrument/detector/hdf_plugin_version |
NDFileHDF5 ver1.10.1 |
|
/measurement/instrument/detector/manufacturer |
FLIR |
|
/measurement/instrument/detector/max_size_x |
3232 |
|
/measurement/instrument/detector/max_size_y |
2426 |
|
/measurement/instrument/detector/model |
Oryx ORX-10G-310S9M |
|
/measurement/instrument/detector/pixel_format |
Mono16 |
|
/measurement/instrument/detector/pixel_size |
6.9 |
μm |
/measurement/instrument/detector/roi/min_x |
0 |
|
/measurement/instrument/detector/roi/min_y |
600 |
|
/measurement/instrument/detector/roi/size_x |
3232 |
|
/measurement/instrument/detector/roi/size_y |
1200 |
|
/measurement/instrument/detector/sdk_version |
2.4.0.143 |
|
/measurement/instrument/detector/serial_number |
21334235 |
|
/measurement/instrument/detector/temperature |
43.5 |
°C |
/measurement/instrument/detector_motor_stack/name |
Camera motors |
|
/measurement/instrument/detector_motor_stack/setup/focus |
-24.47989341085232 |
mm |
/measurement/instrument/detector_motor_stack/setup/rotation |
-0.009512500000000479 |
° |
/measurement/instrument/detector_motor_stack/setup/x |
6.000225000000015 |
mm |
/measurement/instrument/detector_motor_stack/setup/y |
0.0049999999999919 |
mm |
/measurement/instrument/name |
White Beam Tomography |
|
/measurement/instrument/sample_motor_stack/detector_distance |
100.0 |
mm |
/measurement/instrument/sample_motor_stack/name |
microCT sample stages |
|
/measurement/instrument/sample_motor_stack/setup/Center0Deg |
-0.1442190000000192 |
mm |
/measurement/instrument/sample_motor_stack/setup/Center90Deg |
0.00015624999999719336 |
mm |
/measurement/instrument/sample_motor_stack/setup/x |
-2.842170943040401e-14 |
mm |
/measurement/instrument/sample_motor_stack/setup/y |
-12.0000000000001 |
mm |
/measurement/instrument/slits/name |
7-BM-A WB Slits |
|
/measurement/instrument/slits/setup/WB_Slit_H_Center |
-0.4532406250002423 |
mm |
/measurement/instrument/slits/setup/WB_Slit_H_Size |
3.2944812500004845 |
mm |
/measurement/instrument/slits/setup/WB_Slit_V_Center |
-0.299500000000001 |
mm |
/measurement/instrument/slits/setup/WB_Slit_V_Size |
2.60038125 |
mm |
/measurement/instrument/source/beamline |
7-BM |
|
/measurement/instrument/source/current |
102.52231928579201 |
mA |
/measurement/instrument/source/fill_mode |
24s RHB |
|
/measurement/instrument/source/name |
Advanced Photon Source |
|
/measurement/instrument/source/top_up |
Enable |
|
/measurement/instrument/table/name |
Downstream Optical Table |
|
/measurement/instrument/table/setup/DS_Table_X0_Motor_Position |
-7.51449031656 |
mm |
/measurement/instrument/table/setup/DS_Table_X2_Motor_Position |
21.207849999999993 |
mm |
/measurement/instrument/table/setup/DS_Table_Y0_Motor_Position |
7.86892 |
mm |
/measurement/instrument/table/setup/DS_Table_Y1_Motor_Position |
8.76427 |
mm |
/measurement/instrument/table/setup/DS_Table_Y2_Motor_Position |
-27.828875 |
mm |
/measurement/instrument/table/setup/DS_Table_Z2_Motor_Position |
0.561975 |
mm |
/measurement/sample/description_1 |
||
/measurement/sample/description_2 |
||
/measurement/sample/description_3 |
||
/measurement/sample/experiment/proposal |
80644 |
|
/measurement/sample/experiment/safety_id |
Unknown |
|
/measurement/sample/experiment/title |
Imaging microsacle structure in soil core |
|
/measurement/sample/experimenter/email |
||
/measurement/sample/experimenter/institution |
Argonne National Laboratory |
|
/measurement/sample/experimenter/name |
Finfrock |
|
/measurement/sample/experimenter/user_id |
83126 |
|
/measurement/sample/file/full_name |
/data/2022-10-Finfrock-80644/Center_Normal_Scan_Y_012_032.h5 |
|
/measurement/sample/file/name |
Center_Normal_Scan_Y_012 |
|
/measurement/sample/file/path |
/data/2022-10-Finfrock-80644/ |
|
/measurement/sample/name |
||
/process/acquisition/dark_fields/mode |
Start |
|
/process/acquisition/dark_fields/number |
20 |
|
/process/acquisition/dark_fields/value |
0.0 counts |
|
/process/acquisition/end_date |
October 18, 2022 20:27:20 |
|
/process/acquisition/flat_fields/axis |
Both |
|
/process/acquisition/flat_fields/different_flat_exposure |
Different |
|
/process/acquisition/flat_fields/flat_exposure_time |
0.03 |
s |
/process/acquisition/flat_fields/mode |
Start |
|
/process/acquisition/flat_fields/number |
20 |
|
/process/acquisition/flat_fields/sample/in_x |
0.0 |
mm |
/process/acquisition/flat_fields/sample/in_y |
-12.0 |
mm |
/process/acquisition/flat_fields/sample/out_x |
-15.0 |
mm |
/process/acquisition/flat_fields/sample/out_y |
-12.9 |
mm |
/process/acquisition/flat_fields/sample_out_angle |
0.000 |
|
/process/acquisition/flat_fields/sample_out_angle_enable |
No |
|
/process/acquisition/flat_fields/value |
0.0 |
counts |
/process/acquisition/flip_stitch |
No |
|
/process/acquisition/helical_misalignment |
0.0 |
|
/process/acquisition/pixels_y_per_360_deg |
0.0 |
|
/process/acquisition/rotation/num_angles |
3201 |
|
/process/acquisition/rotation/return |
Yes |
|
/process/acquisition/rotation/speed |
0.9072141670564328 |
°/s |
/process/acquisition/rotation/start |
0.0 |
° |
/process/acquisition/rotation/step |
0.05625 |
° |
/process/acquisition/scan_type |
Single |
|
/process/acquisition/start_date |
October 18, 2022 20:22:52 |
APS 7-BM full layout¶
├── defaults
│ │
│ ├── ColorMode (3252,)
│ ├── HDF5FrameLocation (3252,)
│ ├── MW100_ADC_01_Desc (3252,)
│ ├── MW100_ADC_01_Unit (3252,)
│ ├── MW100_ADC_02_Desc (3252,)
│ ├── MW100_ADC_02_Unit (3252,)
│ ├── MW100_ADC_03_Desc (3252,)
│ ├── MW100_ADC_03_Unit (3252,)
│ ├── MW100_ADC_04_Desc (3252,)
│ ├── MW100_ADC_04_Unit (3252,)
│ ├── MW100_ADC_05_Desc (3252,)
│ ├── MW100_ADC_05_Unit (3252,)
│ ├── MW100_ADC_06_Desc (3252,)
│ ├── MW100_ADC_06_Unit (3252,)
│ ├── MW100_ADC_07_Desc (3252,)
│ ├── MW100_ADC_07_Unit (3252,)
│ ├── MW100_ADC_08_Desc (3252,)
│ ├── MW100_ADC_08_Unit (3252,)
│ ├── MW100_ADC_09_Desc (3252,)
│ ├── MW100_ADC_09_Unit (3252,)
│ ├── MW100_ADC_10_Desc (3252,)
│ ├── MW100_ADC_10_Unit (3252,)
│ ├── NDArrayEpicsTSSec (3252,)
│ ├── NDArrayEpicsTSnSec (3252,)
│ ├── NDArrayTimeStamp (3252,)
│ ├── NDArrayUniqueId (3252,)
│ └── timestamp (3252, 5)
├── exchange
│ │
│ ├── data (3201, 1200, 3232)
│ ├── data_dark (20, 1200, 3232)
│ ├── data_gains (11, 1200, 3232)
│ ├── data_white (20, 1200, 3232)
│ ├── gain_exp_times (11,)
│ └── theta (3201,)
├── measurement
│ │
│ ├── ancillary
│ │ │
│ │ ├── BarometricPressure (1,)
│ │ ├── MW100_ADC_01 (3252,)
│ │ ├── MW100_ADC_02 (3252,)
│ │ ├── MW100_ADC_03 (3252,)
│ │ ├── MW100_ADC_04 (3252,)
│ │ ├── MW100_ADC_05 (3252,)
│ │ ├── MW100_ADC_06 (3252,)
│ │ ├── MW100_ADC_07 (3252,)
│ │ ├── MW100_ADC_08 (3252,)
│ │ ├── MW100_ADC_09 (3252,)
│ │ └── MW100_ADC_10 (3252,)
│ ├── instrument
│ │ │
│ │ ├── attenuator_1
│ │ │ │
│ │ │ ├── description (1,)
│ │ │ ├── name (1,)
│ │ │ └── thickness (1,)
│ │ ├── attenuator_2
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ └── filter_unit_text (1,)
│ │ ├── attenuator_3
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ └── filter_unit_text (1,)
│ │ ├── detection_system
│ │ │ │
│ │ │ ├── objective
│ │ │ │ │
│ │ │ │ ├── magnification (1,)
│ │ │ │ ├── resolution (1,)
│ │ │ │ └── tube_length (1,)
│ │ │ └── scintillator
│ │ │ │
│ │ │ ├── active_thickness (1,)
│ │ │ └── type (1,)
│ │ ├── detector
│ │ │ │
│ │ │ ├── acquire_period (1,)
│ │ │ ├── adcore_version (1,)
│ │ │ ├── array_counter (1,)
│ │ │ ├── array_size_x (1,)
│ │ │ ├── array_size_y (1,)
│ │ │ ├── binning_x (1,)
│ │ │ ├── binning_y (1,)
│ │ │ ├── convert_pixel_format (1,)
│ │ │ ├── data_type (1,)
│ │ │ ├── driver_version (1,)
│ │ │ ├── exposure_auto (1,)
│ │ │ ├── exposure_time (1,)
│ │ │ ├── firmware_version (1,)
│ │ │ ├── frame_rate (1,)
│ │ │ ├── frame_rate_enable (1,)
│ │ │ ├── gain (1,)
│ │ │ ├── gain_auto (1,)
│ │ │ ├── hdf_plugin_version (1,)
│ │ │ ├── manufacturer (1,)
│ │ │ ├── max_size_x (1,)
│ │ │ ├── max_size_y (1,)
│ │ │ ├── model (1,)
│ │ │ ├── pixel_format (1,)
│ │ │ ├── pixel_size (1,)
│ │ │ ├── roi
│ │ │ │ │
│ │ │ │ ├── min_x (1,)
│ │ │ │ ├── min_y (1,)
│ │ │ │ ├── size_x (1,)
│ │ │ │ └── size_y (1,)
│ │ │ ├── sdk_version (1,)
│ │ │ ├── serial_number (1,)
│ │ │ └── temperature (1,)
│ │ ├── detector_motor_stack
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── focus (1,)
│ │ │ ├── rotation (1,)
│ │ │ ├── x (1,)
│ │ │ └── y (1,)
│ │ ├── name (1,)
│ │ ├── sample_motor_stack
│ │ │ │
│ │ │ ├── detector_distance (1,)
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── Center0Deg (1,)
│ │ │ ├── Center90Deg (1,)
│ │ │ ├── x (1,)
│ │ │ └── y (1,)
│ │ ├── slits
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── WB_Slit_H_Center (1,)
│ │ │ ├── WB_Slit_H_Size (1,)
│ │ │ ├── WB_Slit_V_Center (1,)
│ │ │ └── WB_Slit_V_Size (1,)
│ │ ├── source
│ │ │ │
│ │ │ ├── beamline (1,)
│ │ │ ├── current (1,)
│ │ │ ├── fill_mode (1,)
│ │ │ ├── name (1,)
│ │ │ └── top_up (1,)
│ │ └── table
│ │ │
│ │ ├── name (1,)
│ │ └── setup
│ │ │
│ │ ├── DS_Table_X0_Motor_Position (1,)
│ │ ├── DS_Table_X2_Motor_Position (1,)
│ │ ├── DS_Table_Y0_Motor_Position (1,)
│ │ ├── DS_Table_Y1_Motor_Position (1,)
│ │ ├── DS_Table_Y2_Motor_Position (1,)
│ │ └── DS_Table_Z2_Motor_Position (1,)
│ └── sample
│ │
│ ├── description_1 (1,)
│ ├── description_2 (1,)
│ ├── description_3 (1,)
│ ├── experiment
│ │ │
│ │ ├── proposal (1,)
│ │ ├── safety_id (1,)
│ │ └── title (1,)
│ ├── experimenter
│ │ │
│ │ ├── email (1,)
│ │ ├── institution (1,)
│ │ ├── name (1,)
│ │ └── user_id (1,)
│ ├── file
│ │ │
│ │ ├── full_name (1,)
│ │ ├── name (1,)
│ │ └── path (1,)
│ └── name (1,)
└── process
└── acquisition
│
├── dark_fields
│ │
│ ├── mode (1,)
│ ├── number (1,)
│ └── value (1,)
├── end_date (1,)
├── flat_fields
│ │
│ ├── axis (1,)
│ ├── different_flat_exposure (1,)
│ ├── flat_exposure_time (1,)
│ ├── mode (1,)
│ ├── number (1,)
│ ├── sample
│ │ │
│ │ ├── in_x (1,)
│ │ ├── in_y (1,)
│ │ ├── out_x (1,)
│ │ └── out_y (1,)
│ ├── sample_out_angle (1,)
│ ├── sample_out_angle_enable (1,)
│ └── value (1,)
├── flip_stitch (1,)
├── helical_misalignment (1,)
├── pixels_y_per_360_deg (1,)
├── rotation
│ │
│ ├── num_angles (1,)
│ ├── return (1,)
│ ├── speed (1,)
│ ├── start (1,)
│ └── step (1,)
├── scan_type (1,)
└── start_date (1,)
Beamline 32-ID nanoCT¶
The full and up-to-date list of meta-data stored at the APS beamline 32-ID is available at DXfile. A meta-data reader is available at hdf reder
APS 32-ID ccalar meta data¶
Meta data name |
Value |
Units |
/measurement/instrument/beam_monitor/name |
Beam Monitor |
|
/measurement/instrument/beam_monitor/setup/x |
39.66749999999998 |
mm |
/measurement/instrument/beam_monitor/setup/x_dial |
39.66749999999998 |
mm |
/measurement/instrument/beam_monitor/setup/y |
67.20000000000012 |
mm |
/measurement/instrument/beam_monitor/setup/y_dial |
53.09200000000011 |
mm |
/measurement/instrument/beam_stop/name |
TXM beam stop |
|
/measurement/instrument/beam_stop/setup/x |
-0.23899800000000004 |
mm |
/measurement/instrument/beam_stop/setup/x_dial |
1.9064169999999998 |
mm |
/measurement/instrument/beam_stop/setup/y |
1.1102230246251565e-16 |
mm |
/measurement/instrument/beam_stop/setup/y_dial |
-0.7870079999999999 |
mm |
/measurement/instrument/condenser/name |
TXM Condenser |
|
/measurement/instrument/condenser/setup/pitch |
-0.00081999999999967 |
mm |
/measurement/instrument/condenser/setup/pitch_dial |
-1.8e-05 |
mm |
/measurement/instrument/condenser/setup/x |
1.839349 |
mm |
/measurement/instrument/condenser/setup/x_dial |
2.8180609999999997 |
mm |
/measurement/instrument/condenser/setup/y |
0.7686649 |
mm |
/measurement/instrument/condenser/setup/y_dial |
-2.4999999999999998e-05 |
mm |
/measurement/instrument/condenser/setup/yaw |
-0.3125449999999999 |
mm |
/measurement/instrument/condenser/setup/yaw_dial |
0.3111 |
mm |
/measurement/instrument/condenser/setup/z |
-287.0 |
mm |
/measurement/instrument/condenser/setup/z_dial |
-17.504999999999995 |
mm |
/measurement/instrument/crl/name |
Compound Refractive Lenses |
|
/measurement/instrument/crl/setup/pitch |
1.7511875000000146 |
mm |
/measurement/instrument/crl/setup/pitch_dial |
-30.327062499999982 |
mm |
/measurement/instrument/crl/setup/table_y |
-39.19999999999996 |
mm |
/measurement/instrument/crl/setup/x |
-2.288000000000001 |
mm |
/measurement/instrument/crl/setup/x_dial |
-2.288000000000001 |
mm |
/measurement/instrument/crl/setup/y |
-4.684500000000078 |
mm |
/measurement/instrument/crl/setup/y_dial |
43.446999999999925 |
mm |
/measurement/instrument/crl/setup/yaw |
0.8499999999999375 |
mm |
/measurement/instrument/crl/setup/yaw_dial |
236.38759999999994 |
mm |
/measurement/instrument/detection_system/objective/magnification |
10xhr |
|
/measurement/instrument/detection_system/objective/resolution |
20.6 |
nm |
/measurement/instrument/detection_system/objective/tube_length |
0.0 |
mm |
/measurement/instrument/detection_system/scintillator/active_thickness |
23.0 |
μm |
/measurement/instrument/detection_system/scintillator/type |
GGG:Eu |
|
/measurement/instrument/detector/acquire_period |
0.042339784000000005 |
s |
/measurement/instrument/detector/adcore_version |
3.11.0 |
|
/measurement/instrument/detector/array_counter |
2057111 |
|
/measurement/instrument/detector/array_size_x |
2048 |
pixel |
/measurement/instrument/detector/array_size_y |
1516 |
pixel |
/measurement/instrument/detector/binning_x |
2 |
|
/measurement/instrument/detector/binning_y |
2 |
|
/measurement/instrument/detector/convert_pixel_format |
Mono16 |
|
/measurement/instrument/detector/data_type |
UInt16 |
|
/measurement/instrument/detector/driver_version |
3.3.0 |
|
/measurement/instrument/detector/exposure_auto |
0 |
|
/measurement/instrument/detector/exposure_time |
0.499994 |
s |
/measurement/instrument/detector/firmware_version |
2011.4.16.0 |
|
/measurement/instrument/detector/frame_rate |
23.618448313293236 |
fps |
/measurement/instrument/detector/frame_rate_enable |
0 |
|
/measurement/instrument/detector/gain |
0.0 |
|
/measurement/instrument/detector/gain_auto |
0 |
|
/measurement/instrument/detector/hdf_plugin_version |
NDFileHDF5 ver1.10.1 |
|
/measurement/instrument/detector/manufacturer |
FLIR |
|
/measurement/instrument/detector/max_size_x |
2660 |
pixel |
/measurement/instrument/detector/max_size_y |
1516 |
pixel |
/measurement/instrument/detector/model |
Blackfly S BFS-PGE-161S7M |
|
/measurement/instrument/detector/pixel_format |
Mono12Packed |
|
/measurement/instrument/detector/pixel_size |
1.51 |
μm |
/measurement/instrument/detector/roi/min_x |
612 |
pixel |
/measurement/instrument/detector/roi/min_y |
0 |
pixel |
/measurement/instrument/detector/roi/size_x |
2048 |
pixel |
/measurement/instrument/detector/roi/size_y |
1516 |
pixel |
/measurement/instrument/detector/sdk_version |
2.4.0.143 |
|
/measurement/instrument/detector/serial_number |
21109025 |
|
/measurement/instrument/detector/temperature |
31.0 |
°C |
/measurement/instrument/detector_motor_stack/name |
32-ID detector motor stack |
|
/measurement/instrument/detector_motor_stack/setup/x |
0.0 |
mm |
/measurement/instrument/detector_motor_stack/setup/x_dial |
-3.0095 |
mm |
/measurement/instrument/detector_motor_stack/setup/y |
0.0 |
mm |
/measurement/instrument/detector_motor_stack/setup/y_dial |
-38.3315 |
mm |
/measurement/instrument/detector_motor_stack/setup/yaw |
0.44 |
mm |
/measurement/instrument/detector_motor_stack/setup/yaw_dial |
0.44 |
mm |
/measurement/instrument/detector_motor_stack/setup/z |
3300.0 |
mm |
/measurement/instrument/detector_motor_stack/setup/z_dial |
5754.27225 |
mm |
/measurement/instrument/diffuser/name |
TXM diffuser |
|
/measurement/instrument/diffuser/setup/x |
0.0 |
mm |
/measurement/instrument/diffuser/setup/x_dial |
42.4953 |
mm |
/measurement/instrument/flight_tube/name |
Flight_tube |
|
/measurement/instrument/flight_tube/setup/z |
117.25999999999976 |
mm |
/measurement/instrument/flight_tube/setup/z_dial |
-1619.0175000000004 |
mm |
/measurement/instrument/mirror/name |
32-ID Mirror |
|
/measurement/instrument/mirror/setup/stripe |
Si stripe selected |
|
/measurement/instrument/mirror/setup/x |
-33.000035000000025 |
mm |
/measurement/instrument/mirror/setup/y |
0.0 |
um |
/measurement/instrument/monochromator/energy |
8.0 |
keV |
/measurement/instrument/monochromator/name |
Si Double Crystal |
|
/measurement/instrument/monochromator/setup/chi2 |
-0.05149750000000708 |
° |
/measurement/instrument/monochromator/setup/chi2_dial |
-10.173733100000007 |
° |
/measurement/instrument/monochromator/setup/flag |
15.0 |
mm |
/measurement/instrument/monochromator/setup/flag_dial |
35.055 |
mm |
/measurement/instrument/monochromator/setup/theta |
14.307760457362393 |
° |
/measurement/instrument/monochromator/setup/theta2 |
-0.3794784094000212 |
° |
/measurement/instrument/monochromator/setup/theta2_dial |
-6.212574196400022 |
° |
/measurement/instrument/monochromator/setup/theta_dial |
14.307716061238043 |
° |
/measurement/instrument/monochromator/setup/x |
0.4000000000000057 |
mm |
/measurement/instrument/monochromator/setup/x2 |
3.9998 |
mm |
/measurement/instrument/monochromator/setup/x2_dial |
3.4998 |
mm |
/measurement/instrument/monochromator/setup/x_dial |
32.50000000000001 |
mm |
/measurement/instrument/monochromator/setup/y |
0.0 |
mm |
/measurement/instrument/monochromator/setup/y1 |
-13.2456320541973 |
mm |
/measurement/instrument/monochromator/setup/y1_dial |
-13.2456320541973 |
mm |
/measurement/instrument/monochromator/setup/y_dial |
2.40008 |
mm |
/measurement/instrument/monochromator/setup/z2 |
124.99999237060547 |
mm |
/measurement/instrument/monochromator/setup/z2_dial |
124.0 |
mm |
/measurement/instrument/name |
TXM |
|
/measurement/instrument/phase_ring/name |
TXM Phase Ring |
|
/measurement/instrument/phase_ring/setup/x |
460.0 |
mm |
/measurement/instrument/phase_ring/setup/x_dial |
475.85225 |
mm |
/measurement/instrument/phase_ring/setup/y |
-6.0 |
mm |
/measurement/instrument/phase_ring/setup/y_dial |
0.7357909999999999 |
mm |
/measurement/instrument/phase_ring/setup/z |
117.25999999999976 |
mm |
/measurement/instrument/phase_ring/setup/z_dial |
-1619.0175000000004 |
mm |
/measurement/instrument/pin_hole/name |
TXM Pin Hole |
|
/measurement/instrument/pin_hole/setup/x |
-6.990000000000146 |
mm |
/measurement/instrument/pin_hole/setup/x_dial |
2.839700000000146 |
mm |
/measurement/instrument/pin_hole/setup/y |
0.0 |
mm |
/measurement/instrument/pin_hole/setup/y_dial |
-0.8716250000000048 |
mm |
/measurement/instrument/sample_environment/furnace/d |
0.0 |
|
/measurement/instrument/sample_environment/furnace/i |
0.0 |
|
/measurement/instrument/sample_environment/furnace/p |
0.0 |
|
/measurement/instrument/sample_environment/furnace/pid_mode |
0 |
|
/measurement/instrument/sample_environment/furnace/ramp_rate |
0.0 |
°C/s |
/measurement/instrument/sample_environment/furnace/ramp_temperature |
0.0 |
°C |
/measurement/instrument/sample_environment/furnace/set_point |
0.0 |
°C |
/measurement/instrument/sample_environment/furnace/temperature |
0.0 |
°C |
/measurement/instrument/sample_environment/furnace/thermocouple |
888888.0 |
°C |
/measurement/instrument/sample_environment/furnace/update_rate |
7 |
s |
/measurement/instrument/sample_motor_stack/name |
TXM sample stages stack |
|
/measurement/instrument/sample_motor_stack/setup/rotary |
180.31080508474574 |
mm |
/measurement/instrument/sample_motor_stack/setup/rotary_dial |
50.62080508474574 |
mm |
/measurement/instrument/sample_motor_stack/setup/top/x |
0.0 |
mm |
/measurement/instrument/sample_motor_stack/setup/top/x_dial |
2.0489669999999944 |
mm |
/measurement/instrument/sample_motor_stack/setup/top/z |
0.0 |
mm |
/measurement/instrument/sample_motor_stack/setup/top/z_dial |
-0.35613400000000706 |
mm |
/measurement/instrument/sample_motor_stack/setup/x |
-9761.289999999997 |
mm |
/measurement/instrument/sample_motor_stack/setup/x_dial |
14321.829999999998 |
mm |
/measurement/instrument/sample_motor_stack/setup/y |
6.154020999999631 |
mm |
/measurement/instrument/sample_motor_stack/setup/y_dial |
125.25354720000038 |
mm |
/measurement/instrument/slits/horizontal/setup/Center |
0.04041788149999978 |
mm |
/measurement/instrument/slits/horizontal/setup/size |
2.2496012794794025 |
mm |
/measurement/instrument/slits/name |
32-ID slits |
|
/measurement/instrument/slits/vertical/setup/center |
-0.47999999999999954 |
mm |
/measurement/instrument/slits/vertical/setup/size |
0.7990000494718017 |
mm |
/measurement/instrument/source/beamline |
32-ID |
|
/measurement/instrument/source/current |
101.723080369204 |
mA |
/measurement/instrument/source/energy |
25.746719360351562 |
keV |
/measurement/instrument/source/fill_mode |
0+24x1 RHB |
|
/measurement/instrument/source/gap |
179.99975 |
mm |
/measurement/instrument/source/name |
Advanced Photon Source |
|
/measurement/instrument/source/top_up |
Enable |
|
/measurement/instrument/zone_plate/description |
FZP2 |
|
/measurement/instrument/zone_plate/outermost_zone_width |
50 |
|
/measurement/instrument/zone_plate/setup/x |
-3.1100590000000263 |
mm |
/measurement/instrument/zone_plate/setup/x_dial |
3.769401000000016 |
mm |
/measurement/instrument/zone_plate/setup/y |
0.0 |
mm |
/measurement/instrument/zone_plate/setup/y_dial |
0.8195010000000017 |
mm |
/measurement/instrument/zone_plate/setup/z |
59.124 |
mm |
/measurement/instrument/zone_plate/setup/z_dial |
-43.51546299999998 |
mm |
/measurement/sample/description_1 |
Unknown |
|
/measurement/sample/description_2 |
Unknown |
|
/measurement/sample/description_3 |
Unknown |
|
/measurement/sample/experiment/proposal |
74240 |
|
/measurement/sample/experiment/safety_id |
Unknown |
|
/measurement/sample/experiment/title |
Replacement of calcium carbonate (CaCO3) polymorphs by lead, zinc, and cadmium carbonates |
|
/measurement/sample/experimenter/email |
||
/measurement/sample/experimenter/institution |
Argonne National Laboratory |
|
/measurement/sample/experimenter/name |
Fenter |
|
/measurement/sample/experimenter/user_id |
50607 |
|
/measurement/sample/file/full_name |
/local/dataraid/2023-03/Fenter/Calcite_sr5per_2_abs_192.h5 |
|
/measurement/sample/file/name |
Calcite_sr5per_2_abs |
|
/measurement/sample/file/path |
/local/dataraid/2023-03/Fenter/ |
|
/measurement/sample/name |
Unknown |
|
/process/acquisition/dark_fields/mode |
None |
|
/process/acquisition/dark_fields/number |
20 |
|
/process/acquisition/dark_fields/value |
0.0 |
counts |
/process/acquisition/end_date |
2023-03-22T11:28:11-0500 |
|
/process/acquisition/flat_fields/axis |
Y |
|
/process/acquisition/flat_fields/different_flat_exposure |
Same |
|
/process/acquisition/flat_fields/flat_exposure_time |
0.0 |
s |
/process/acquisition/flat_fields/mode |
Start |
|
/process/acquisition/flat_fields/number |
20 |
|
/process/acquisition/flat_fields/sample/in_x |
0.0 |
mm |
/process/acquisition/flat_fields/sample/in_y |
0.0 |
mm |
/process/acquisition/flat_fields/sample/out_x |
2.0 |
mm |
/process/acquisition/flat_fields/sample/out_y |
2.0 |
mm |
/process/acquisition/flat_fields/sample_out_angle |
90.000 |
|
/process/acquisition/flat_fields/sample_out_angle_enable |
Yes |
|
/process/acquisition/flat_fields/value |
0.0 |
counts |
/process/acquisition/flip_stitch |
No |
|
/process/acquisition/rotation/num_angles |
1501 |
|
/process/acquisition/rotation/return |
No |
|
/process/acquisition/rotation/speed |
0.23213248345273438 |
°/s |
/process/acquisition/rotation/start |
0.0 |
° |
/process/acquisition/rotation/step |
0.12012711864406779 |
° |
/process/acquisition/scan_type |
Single |
|
/process/acquisition/start_date |
2023-03-22T11:14:49-0500 |
APS 32-ID Full layout¶
├── defaults
│ │
│ ├── ColorMode (1521,)
│ ├── HDF5FrameLocation (1521,)
│ ├── NDArrayEpicsTSSec (1521,)
│ ├── NDArrayEpicsTSnSec (1521,)
│ ├── NDArrayTimeStamp (1521,)
│ ├── NDArrayUniqueId (1521,)
│ └── timestamp (1521, 5)
├── exchange
│ │
│ ├── data (1501, 1516, 2048)
│ ├── data2 (1516, 2048)
│ ├── data_dark (1, 1516, 2048)
│ ├── data_white (20, 1516, 2048)
│ └── theta (1501,)
├── measurement
│ │
│ ├── instrument
│ │ │
│ │ ├── beam_monitor
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ └── y_dial (1,)
│ │ ├── beam_stop
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ └── y_dial (1,)
│ │ ├── condenser
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── pitch (1,)
│ │ │ ├── pitch_dial (1,)
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ ├── y_dial (1,)
│ │ │ ├── yaw (1,)
│ │ │ ├── yaw_dial (1,)
│ │ │ ├── z (1,)
│ │ │ └── z_dial (1,)
│ │ ├── crl
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── pitch (1,)
│ │ │ ├── pitch_dial (1,)
│ │ │ ├── table_y (1,)
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ ├── y_dial (1,)
│ │ │ ├── yaw (1,)
│ │ │ └── yaw_dial (1,)
│ │ ├── detection_system
│ │ │ │
│ │ │ ├── objective
│ │ │ │ │
│ │ │ │ ├── magnification (1,)
│ │ │ │ ├── resolution (1,)
│ │ │ │ └── tube_length (1,)
│ │ │ └── scintillator
│ │ │ │
│ │ │ ├── active_thickness (1,)
│ │ │ └── type (1,)
│ │ ├── detector
│ │ │ │
│ │ │ ├── acquire_period (1,)
│ │ │ ├── adcore_version (1,)
│ │ │ ├── array_counter (1,)
│ │ │ ├── array_size_x (1,)
│ │ │ ├── array_size_y (1,)
│ │ │ ├── binning_x (1,)
│ │ │ ├── binning_y (1,)
│ │ │ ├── convert_pixel_format (1,)
│ │ │ ├── data_type (1,)
│ │ │ ├── driver_version (1,)
│ │ │ ├── exposure_auto (1,)
│ │ │ ├── exposure_time (1,)
│ │ │ ├── firmware_version (1,)
│ │ │ ├── frame_rate (1,)
│ │ │ ├── frame_rate_enable (1,)
│ │ │ ├── gain (1,)
│ │ │ ├── gain_auto (1,)
│ │ │ ├── hdf_plugin_version (1,)
│ │ │ ├── manufacturer (1,)
│ │ │ ├── max_size_x (1,)
│ │ │ ├── max_size_y (1,)
│ │ │ ├── model (1,)
│ │ │ ├── pixel_format (1,)
│ │ │ ├── pixel_size (1,)
│ │ │ ├── roi
│ │ │ │ │
│ │ │ │ ├── min_x (1,)
│ │ │ │ ├── min_y (1,)
│ │ │ │ ├── size_x (1,)
│ │ │ │ └── size_y (1,)
│ │ │ ├── sdk_version (1,)
│ │ │ ├── serial_number (1,)
│ │ │ └── temperature (1,)
│ │ ├── detector_motor_stack
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ ├── y_dial (1,)
│ │ │ ├── yaw (1,)
│ │ │ ├── yaw_dial (1,)
│ │ │ ├── z (1,)
│ │ │ └── z_dial (1,)
│ │ ├── diffuser
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── x (1,)
│ │ │ └── x_dial (1,)
│ │ ├── flight_tube
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── z (1,)
│ │ │ └── z_dial (1,)
│ │ ├── mirror
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── stripe (1,)
│ │ │ ├── x (1,)
│ │ │ └── y (1,)
│ │ ├── monochromator
│ │ │ │
│ │ │ ├── energy (1,)
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── chi2 (1,)
│ │ │ ├── chi2_dial (1,)
│ │ │ ├── flag (1,)
│ │ │ ├── flag_dial (1,)
│ │ │ ├── theta (1,)
│ │ │ ├── theta2 (1,)
│ │ │ ├── theta2_dial (1,)
│ │ │ ├── theta_dial (1,)
│ │ │ ├── x (1,)
│ │ │ ├── x2 (1,)
│ │ │ ├── x2_dial (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ ├── y1 (1,)
│ │ │ ├── y1_dial (1,)
│ │ │ ├── y_dial (1,)
│ │ │ ├── z2 (1,)
│ │ │ └── z2_dial (1,)
│ │ ├── name (1,)
│ │ ├── phase_ring
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ ├── y_dial (1,)
│ │ │ ├── z (1,)
│ │ │ └── z_dial (1,)
│ │ ├── pin_hole
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ └── y_dial (1,)
│ │ ├── sample_environment
│ │ │ └── furnace
│ │ │ │
│ │ │ ├── d (1,)
│ │ │ ├── i (1,)
│ │ │ ├── p (1,)
│ │ │ ├── pid_mode (1,)
│ │ │ ├── ramp_rate (1,)
│ │ │ ├── ramp_temperature (1,)
│ │ │ ├── set_point (1,)
│ │ │ ├── temperature (1,)
│ │ │ ├── thermocouple (1,)
│ │ │ └── update_rate (1,)
│ │ ├── sample_motor_stack
│ │ │ │
│ │ │ ├── name (1,)
│ │ │ └── setup
│ │ │ │
│ │ │ ├── rotary (1,)
│ │ │ ├── rotary_dial (1,)
│ │ │ ├── top
│ │ │ │ │
│ │ │ │ ├── x (1,)
│ │ │ │ ├── x_dial (1,)
│ │ │ │ ├── z (1,)
│ │ │ │ └── z_dial (1,)
│ │ │ ├── x (1,)
│ │ │ ├── x_dial (1,)
│ │ │ ├── y (1,)
│ │ │ └── y_dial (1,)
│ │ ├── slits
│ │ │ │
│ │ │ ├── horizontal
│ │ │ │ └── setup
│ │ │ │ │
│ │ │ │ ├── Center (1,)
│ │ │ │ └── size (1,)
│ │ │ ├── name (1,)
│ │ │ └── vertical
│ │ │ └── setup
│ │ │ │
│ │ │ ├── center (1,)
│ │ │ └── size (1,)
│ │ ├── source
│ │ │ │
│ │ │ ├── beamline (1,)
│ │ │ ├── current (1,)
│ │ │ ├── energy (1,)
│ │ │ ├── fill_mode (1,)
│ │ │ ├── gap (1,)
│ │ │ ├── name (1,)
│ │ │ └── top_up (1,)
│ │ └── zone_plate
│ │ │
│ │ ├── description (1,)
│ │ ├── outermost_zone_width (1,)
│ │ └── setup
│ │ │
│ │ ├── x (1,)
│ │ ├── x_dial (1,)
│ │ ├── y (1,)
│ │ ├── y_dial (1,)
│ │ ├── z (1,)
│ │ └── z_dial (1,)
│ └── sample
│ │
│ ├── description_1 (1,)
│ ├── description_2 (1,)
│ ├── description_3 (1,)
│ ├── experiment
│ │ │
│ │ ├── proposal (1,)
│ │ ├── safety_id (1,)
│ │ └── title (1,)
│ ├── experimenter
│ │ │
│ │ ├── email (1,)
│ │ ├── institution (1,)
│ │ ├── name (1,)
│ │ └── user_id (1,)
│ ├── file
│ │ │
│ │ ├── full_name (1,)
│ │ ├── name (1,)
│ │ └── path (1,)
│ └── name (1,)
└── process
└── acquisition
│
├── dark_fields
│ │
│ ├── mode (1,)
│ ├── number (1,)
│ └── value (1,)
├── end_date (1,)
├── flat_fields
│ │
│ ├── axis (1,)
│ ├── different_flat_exposure (1,)
│ ├── flat_exposure_time (1,)
│ ├── mode (1,)
│ ├── number (1,)
│ ├── sample
│ │ │
│ │ ├── in_x (1,)
│ │ ├── in_y (1,)
│ │ ├── out_x (1,)
│ │ └── out_y (1,)
│ ├── sample_out_angle (1,)
│ ├── sample_out_angle_enable (1,)
│ └── value (1,)
├── flip_stitch (1,)
├── rotation
│ │
│ ├── num_angles (1,)
│ ├── return (1,)
│ ├── speed (1,)
│ ├── start (1,)
│ └── step (1,)
├── scan_type (1,)
└── start_date (1,)
NSLS-II¶
The National Synchrotron Light Source II (NSLS-II) nano tomography instrument generates HDF files. A meta-data reader is available at hdf reder
nanoTomo scalar meta data¶
Meta data name |
Value |
Units |
Magnification |
297.74961267203344 |
|
Pixel Size |
43.66084604892265 |
nm |
X_eng |
8.290000000000001 |
|
acquisition_period |
0.05 |
|
ang_range |
200 |
|
binning |
1 |
|
exposure_time |
0.04 |
|
filters |
None |
|
note |
47_VGCF_NMC3D_xanesNi_63_energy=8.29 |
|
r_ini |
0.0 |
|
scan_id |
2877 |
|
scan_time |
2022-10-18 14:19:00.445353 |
|
slew_velocity |
6 |
|
start_angle |
None |
|
uid |
25ef5452-b0f3-4a3c-a6a0-80d3e040cd5c |
|
x_ini |
-1859.9990000000003 |
|
y_ini |
-1778.9999999999998 |
|
z_ini |
-615.0000000000001 |
nanoTomo full layout¶
│
├── Magnification ()
├── Pixel Size ()
├── X_eng ()
├── acquisition_period ()
├── ang_range ()
├── angle (601,)
├── binning ()
├── exposure_time ()
├── filters ()
├── img_bkg (20, 1080, 1280)
├── img_bkg_avg (1, 1080, 1280)
├── img_dark (20, 1080, 1280)
├── img_dark_avg (1, 1080, 1280)
├── img_tomo (601, 1080, 1280)
├── note ()
├── r_ini ()
├── scan_id ()
├── scan_time ()
├── slew_velocity ()
├── start_angle ()
├── uid ()
├── x_ini ()
├── y_ini ()
└── z_ini ()
ESRF¶
European Synchrotron Radiation Facility (ESRF) uses NeXus NXTomo definition to store data and meta-data in a HDF file. The raw data file collected at the beamline are converted in a NeXus file using nxtomomill. Below is the output of nxtomomill version a3173f887d97ede9b4947bc984d34b913a7cc255. A meta-data reader is available at hdf reder
ID-19 scalar meta data¶
Meta data name |
Value |
Units |
/entry0000/bliss_original_files |
/data/2023-08/decarlo/ESRF/align/in1089_align.h5 |
|
/entry0000/end_time |
2023-03-01T10:23:56.262594+01:00 |
|
/entry0000/instrument/beam/incident_energy |
19.5 |
keV |
/entry0000/instrument/detector/distance |
1.1965000000000001 |
m |
/entry0000/instrument/detector/estimated_cor_from_motor |
699.7356554190684 |
pixel |
/entry0000/instrument/detector/field_of_view |
Half |
|
/entry0000/instrument/detector/tomo_n |
4600 |
|
/entry0000/instrument/detector/x_flipped |
False |
|
/entry0000/instrument/detector/x_pixel_size |
6.430999999999999e-07 |
m |
/entry0000/instrument/detector/y_flipped |
True |
|
/entry0000/instrument/detector/y_pixel_size |
6.430999999999999e-07 |
m |
/entry0000/instrument/source/name |
ESRF |
|
/entry0000/instrument/source/probe |
x-ray |
|
/entry0000/instrument/source/type |
Synchrotron X-ray Source |
|
/entry0000/sample/name |
align |
|
/entry0000/start_time |
2023-03-01T10:15:11.366386+01:00 |
|
/entry0000/title |
0001 |
ID-19 full layout¶
entry0000
│
├── beam
│ └── incident_energy ()
├── bliss_original_files (1,)
├── control
│ └── data (4840,)
├── data
│ │
│ ├── data (4840, 2160, 2560)
│ ├── image_key (4840,)
│ ├── image_key_control (4840,)
│ └── rotation_angle (4840,)
├── end_time ()
├── instrument
│ │
│ ├── beam
│ │ └── incident_energy ()
│ ├── detector
│ │ │
│ │ ├── count_time (4840,)
│ │ ├── data (4840, 2160, 2560)
│ │ ├── distance ()
│ │ ├── estimated_cor_from_motor ()
│ │ ├── field_of_view ()
│ │ ├── image_key (4840,)
│ │ ├── image_key_control (4840,)
│ │ ├── tomo_n ()
│ │ ├── x_flipped ()
│ │ ├── x_pixel_size ()
│ │ ├── y_flipped ()
│ │ └── y_pixel_size ()
│ └── source
│ │
│ ├── name ()
│ ├── probe ()
│ └── type ()
├── sample
│ │
│ ├── name ()
│ ├── rotation_angle (4840,)
│ ├── x_translation (4840,)
│ ├── y_translation (4840,)
│ └── z_translation (4840,)
├── start_time ()
└── title ()
DESY¶
Deutsches Elektronen-Synchrotron (DESY) Petra III beamline P07 uses NeXus NXTomo definition to store data and meta-data in a HDF file. A meta-data reader is available at hdf reder
P07 scalar meta data¶
Meta data name |
Value |
Units |
/entry/beamline/experiment |
microtomography |
|
/entry/beamline/name |
P07 HEMS EH4 |
|
/entry/hardware/camera/bin |
1.0 |
|
/entry/hardware/camera/exptime |
120.0 |
|
/entry/hardware/camera/magnification |
5.040330410003662 |
|
/entry/hardware/camera/pixelsize |
0.006399999838322401 |
|
/entry/hardware/camera/resolution |
3.8918843269348145 |
|
/entry/hardware/camera/roi_height |
2151.0 |
|
/entry/hardware/camera/roi_width |
5120.0 |
|
/entry/hardware/camera/sensorsize_x |
5120 |
|
/entry/hardware/camera/sensorsize_y |
3840 |
|
/entry/scan/mode |
360.72 |
|
/entry/scan/n_angle |
501.0 |
|
/entry/scan/n_dark |
4.0 |
|
/entry/scan/n_ref |
5.0 |
|
/entry/scan/setup/o_ccd_dist |
799.9865 |
|
/entry/scan/setup/p07_energy |
67000.0 |
|
/entry/scan/setup/s_stage_x |
7.627620410546353 |
|
/entry/scan/setup/s_stage_z |
-28.405404649222458 |
P07 full layout¶
entry
│
├── beamline
│ │
│ ├── experiment (1,)
│ └── name (1,)
├── hardware
│ │
│ ├── P07_EH4_MAPPER
│ │ └── thermohygro_mapper
│ │ │
│ │ ├── Humidity
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── Pressure
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ └── Temperature
│ │ │
│ │ ├── time (149,)
│ │ └── value (149,)
│ ├── P07_EH4_TOMO
│ │ └── thermohygro_tomo
│ │ │
│ │ ├── Humidity
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── Pressure
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ └── Temperature
│ │ │
│ │ ├── time (149,)
│ │ └── value (149,)
│ ├── P07_Frontend
│ │ │
│ │ ├── gap
│ │ │ └── Gap
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── pr_slit1_vgap
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── pr_slit1_voffset
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── pr_slit2_hleft
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── pr_slit2_hright
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── pr_slit2_vgap
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── pr_slit2_voffset
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── shutter_x
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ └── shutter_z
│ │ └── Position
│ │ │
│ │ ├── time (149,)
│ │ └── value (149,)
│ ├── P07_OH1
│ │ │
│ │ ├── dcm_1st_bend
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_1st_pitch
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_1st_roll
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_1st_yaw
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_2nd_bend
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_2nd_lateral
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_2nd_longitudinal
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_2nd_pitch
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_2nd_roll
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── dcm_2nd_yaw
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_IntMon_Motor
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_lat1
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_lat2
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_pitch1_rx
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_pitch2_rx
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_roll1_ry
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_roll2_ry
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_vert1
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_vert2
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_yaw1_rz
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── oh1_LT_yaw2_rz
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── sbm_lateral
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── sbm_pitch
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── sbm_roll
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ └── sbm_yaw
│ │ └── Position
│ │ │
│ │ ├── time (149,)
│ │ └── value (149,)
│ ├── P07_OH3_EH3
│ │ │
│ │ ├── slit_tomo_bottom
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── slit_tomo_left
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ ├── slit_tomo_right
│ │ │ └── Position
│ │ │ │
│ │ │ ├── time (149,)
│ │ │ └── value (149,)
│ │ └── slit_tomo_top
│ │ └── Position
│ │ │
│ │ ├── time (149,)
│ │ └── value (149,)
│ ├── beam_current
│ │ └── current
│ │ │
│ │ ├── time (594,)
│ │ └── value (594,)
│ └── camera
│ │
│ ├── bin (1,)
│ ├── exptime (1,)
│ ├── magnification (1,)
│ ├── pixelsize (1,)
│ ├── resolution (1,)
│ ├── roi_height (1,)
│ ├── roi_width (1,)
│ ├── sensorsize_x (1,)
│ └── sensorsize_y (1,)
└── scan
│
├── data
│ │
│ ├── image_file
│ │ │
│ │ ├── time (515,)
│ │ └── value (515,)
│ ├── image_key
│ │ │
│ │ ├── time (515,)
│ │ └── value (515,)
│ ├── s_rot
│ │ │
│ │ ├── time (511,)
│ │ └── value (511,)
│ ├── s_stage_x
│ │ │
│ │ ├── time (511,)
│ │ └── value (511,)
│ └── s_stage_z
│ │
│ ├── time (501,)
│ └── value (501,)
├── mode (1,)
├── n_angle (1,)
├── n_dark (1,)
├── n_ref (1,)
└── setup
│
├── o_ccd_dist (1,)
├── p07_energy (1,)
├── s_stage_x (1,)
└── s_stage_z (1,)
Diamond¶
Diamond Light Source uses NeXus NXTomo definition to store data and meta-data in a HDF file. A meta-data reader is available at hdf reder
ID12 scalar meta data¶
Meta data name |
Value |
Units |
/entry1/before_scan/cam1/cam1_roll |
-0.00300197 |
|
/entry1/before_scan/cam1/cam1_x |
140.56 |
|
/entry1/before_scan/cam1/cam1_z |
-96.12984375 |
|
/entry1/before_scan/dcm1_cap_1/dcm1_cap_1 |
73.03 |
|
/entry1/before_scan/dcm1_cap_2/dcm1_cap_2 |
74.235 |
|
/entry1/before_scan/det_cfg/cam_adc_mode |
One ADC |
|
/entry1/before_scan/det_cfg/cam_bin_x |
1 |
|
/entry1/before_scan/det_cfg/cam_bin_y |
1 |
|
/entry1/before_scan/det_cfg/cam_img_size_x |
2560 |
|
/entry1/before_scan/det_cfg/cam_img_size_y |
2160 |
|
/entry1/before_scan/det_cfg/cam_model |
pco.edge |
|
/entry1/before_scan/det_cfg/cam_pixel_rate |
286000000 Hz |
|
/entry1/before_scan/det_cfg/cam_roi_min_x |
0 |
|
/entry1/before_scan/det_cfg/cam_roi_min_y |
0 |
|
/entry1/before_scan/det_cfg/cam_roi_size_x |
2560 |
|
/entry1/before_scan/det_cfg/cam_roi_size_y |
2160 |
|
/entry1/before_scan/det_cfg/cam_sensor_size_x |
2560 |
|
/entry1/before_scan/det_cfg/cam_sensor_size_y |
2160 |
|
/entry1/before_scan/det_cfg/cam_timestamp_mode |
BCD+ASCII |
|
/entry1/before_scan/det_cfg/readout_time_sec |
0.011 |
|
/entry1/before_scan/f1 |
clear |
|
/entry1/before_scan/f2 |
clear |
|
/entry1/before_scan/flyscan_cfg/tomography_cmd |
i12tomoFlyScan(closeShutterAfterScan=True, description=frame_M2, exposureTime=0.025, extraFlatsAtEnd=False, helical_axis_stage=None, imagesPerDark=20, imagesPerFlat=50, inBeamPosition=0.8, outOfBeamPosition=30.0, start=0.0, step=0.1, stop=180, vetoFlatsDarksAtStart=False, zebra3_cfg_fpath=/dls_sw/i12/epics/zebra/pilatus_flyscan_time_compare.zeb) |
|
/entry1/before_scan/flyscan_cfg/tomography_flyscan_det |
flyScanDetector |
|
/entry1/before_scan/flyscan_cfg/tomography_flyscan_theta |
zebraSM1 |
|
/entry1/before_scan/flyscan_cfg/tomography_shutter |
eh1shtr |
|
/entry1/before_scan/flyscan_cfg/tomography_translation |
ss1_x |
|
/entry1/before_scan/mc1_bragg/mc1_bragg |
-937.60672678678 |
|
/entry1/before_scan/mc2/mc2_bragg |
-956.60716546391 |
|
/entry1/before_scan/mc2/mc2_z |
1456.0001347856 |
|
/entry1/before_scan/mc2_bragg/mc2_bragg |
-956.60716546391 |
|
/entry1/before_scan/s1/s1_bottom |
-0.99995 |
|
/entry1/before_scan/s1/s1_in |
-4.4989 |
|
/entry1/before_scan/s1/s1_out |
4.49955 |
|
/entry1/before_scan/s1/s1_t1 |
22.1 |
|
/entry1/before_scan/s1/s1_t2 |
21.6 |
|
/entry1/before_scan/s1/s1_top |
1.00005 |
|
/entry1/before_scan/s1/s1_xc |
0.000375 |
|
/entry1/before_scan/s1/s1_xs |
8.9985 |
|
/entry1/before_scan/s1/s1_yc |
5e-05 |
|
/entry1/before_scan/s1/s1_ys |
2.0 |
|
/entry1/before_scan/s2/s2_bottom |
47.045 |
|
/entry1/before_scan/s2/s2_in |
-7.7895 |
|
/entry1/before_scan/s2/s2_out |
7.2105 |
|
/entry1/before_scan/s2/s2_top |
54.034 |
|
/entry1/before_scan/s2/s2_xc |
0.0 |
|
/entry1/before_scan/s2/s2_xs |
15.0 |
|
/entry1/before_scan/s2/s2_yc |
50.0 |
|
/entry1/before_scan/s2/s2_ys |
6.999 |
|
/entry1/before_scan/s3/s3_bottom |
-1.0 |
|
/entry1/before_scan/s3/s3_in |
-1.0 |
|
/entry1/before_scan/s3/s3_out |
1.0 |
|
/entry1/before_scan/s3/s3_top |
1.0 |
|
/entry1/before_scan/s3/s3_xc |
0.0 |
|
/entry1/before_scan/s3/s3_xs |
2.0 |
|
/entry1/before_scan/s3/s3_y |
-150.0 |
|
/entry1/before_scan/s3/s3_yc |
0.0 |
|
/entry1/before_scan/s3/s3_ys |
2.0 |
|
/entry1/before_scan/ss1/ss1_phi |
0.000135 |
|
/entry1/before_scan/ss1/ss1_rx |
0.001172834396 |
|
/entry1/before_scan/ss1/ss1_rz |
-0.01147762649 |
|
/entry1/before_scan/ss1/ss1_theta |
0.0 |
|
/entry1/before_scan/ss1/ss1_tx |
0.1 |
|
/entry1/before_scan/ss1/ss1_tz |
-2.7 |
|
/entry1/before_scan/ss1/ss1_x |
0.8 |
|
/entry1/before_scan/ss1/ss1_y1 |
48.9986 |
|
/entry1/before_scan/ss1/ss1_y2 |
-0.0001 |
|
/entry1/before_scan/ss1/ss1_y3 |
13.4 |
|
/entry1/before_scan/ss2/ss2_rx |
0.0 |
|
/entry1/before_scan/ss2/ss2_theta |
-0.003000000026 |
|
/entry1/before_scan/ss2/ss2_x |
-0.003001199802 |
|
/entry1/before_scan/ss2/ss2_y |
-400.001007080078 |
|
/entry1/before_scan/ss2/ss2_z |
-0.001000000047 |
|
/entry1/before_scan/t3/t3_m1y |
40.096 |
|
/entry1/before_scan/t3/t3_m1z |
1000.00078125 |
|
/entry1/before_scan/t3/t3_m2y |
50.998 |
|
/entry1/before_scan/t3/t3_m2z |
1399.9995 |
|
/entry1/before_scan/t3/t3_m3rx |
0.0 |
|
/entry1/before_scan/t3/t3_m3ry |
45.0 |
|
/entry1/before_scan/t3/t3_m3rz |
0.0 |
|
/entry1/before_scan/t3/t3_m3y |
-0.025 |
|
/entry1/before_scan/t3/t3_m3z |
1549.99918125 |
|
/entry1/before_scan/t3/t3_m4rx |
1.19998 |
|
/entry1/before_scan/t3/t3_m4ry |
-0.40002 |
|
/entry1/before_scan/t3/t3_m4x |
95.147 |
|
/entry1/before_scan/t3/t3_m4y |
8.9 |
|
/entry1/before_scan/t3/t3_x |
1349.393 |
|
/entry1/before_scan/t7/t7_m1z |
1200.0 |
|
/entry1/before_scan/t7/t7_m2rx |
0.324 |
|
/entry1/before_scan/t7/t7_m2ry |
0.87496875 |
|
/entry1/before_scan/t7/t7_m2x |
-23.901 |
|
/entry1/before_scan/t7/t7_m2y |
-11.053 |
|
/entry1/before_scan/t7/t7_m2z |
-0.5 |
|
/entry1/before_scan/t7/t7_m3rx |
0.0 |
|
/entry1/before_scan/t7/t7_m3ry |
0.0 |
|
/entry1/before_scan/t7/t7_m3rz |
0.0 |
|
/entry1/before_scan/t7/t7_m3z |
1331.0 |
|
/entry1/before_scan/t7/t7_x |
-0.008 |
|
/entry1/before_scan/t7/t7_y |
42.977 |
|
/entry1/end_time |
2022-05-09T19:40:22.244627+01:00 |
|
/entry1/entry_identifier |
110809 |
|
/entry1/experiment_identifier |
cm31132-2 |
|
/entry1/instrument/flyScanDetector/local_name |
flyScanDetector |
|
/entry1/instrument/name |
i12 |
|
/entry1/instrument/source/current |
298.1787 |
mA |
/entry1/instrument/source/energy |
3.0009 |
GeV |
/entry1/instrument/source/name |
DLS |
|
/entry1/instrument/source/probe |
x-ray |
|
/entry1/instrument/source/type |
Synchrotron X-Ray Source |
|
/entry1/program_name |
GDA 9.20.0 |
|
/entry1/scan_command |
scan zebraSM1 (0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0) image_key zebraContinuousMoveController flyScanDetector 0.025 |
|
/entry1/scan_dimensions |
1871 |
|
/entry1/scan_identifier |
207a99a0-fe96-4db3-9611-796b9eb06719 |
|
/entry1/start_time |
2022-05-09T19:38:44.223666+01:00 |
|
/entry1/title |
frame_M2 |
|
/entry1/tomo_entry/definition |
NXtomo |
|
/entry1/tomo_entry/instrument/detector/distance |
nan undefined |
|
/entry1/tomo_entry/instrument/detector/x_pixel_size |
nan undefined |
|
/entry1/tomo_entry/instrument/detector/x_rotation_axis_pixel_position |
nan pixel |
|
/entry1/tomo_entry/instrument/detector/y_pixel_size |
nan undefined |
|
/entry1/tomo_entry/instrument/detector/y_rotation_axis_pixel_position |
nan pixel |
|
/entry1/user01/username |
lpq70547 |
ID12 full layout¶
entry1
│
├── before_scan
│ │
│ ├── cam1
│ │ │
│ │ ├── cam1_roll ()
│ │ ├── cam1_x ()
│ │ └── cam1_z ()
│ ├── dcm1_cap_1
│ │ └── dcm1_cap_1 ()
│ ├── dcm1_cap_2
│ │ └── dcm1_cap_2 ()
│ ├── det_cfg
│ │ │
│ │ ├── cam_adc_mode ()
│ │ ├── cam_bin_x ()
│ │ ├── cam_bin_y ()
│ │ ├── cam_img_size_x ()
│ │ ├── cam_img_size_y ()
│ │ ├── cam_model ()
│ │ ├── cam_pixel_rate ()
│ │ ├── cam_roi_min_x ()
│ │ ├── cam_roi_min_y ()
│ │ ├── cam_roi_size_x ()
│ │ ├── cam_roi_size_y ()
│ │ ├── cam_sensor_size_x ()
│ │ ├── cam_sensor_size_y ()
│ │ ├── cam_timestamp_mode ()
│ │ └── readout_time_sec ()
│ ├── f1 (1,)
│ ├── f2 (1,)
│ ├── flyscan_cfg
│ │ │
│ │ ├── tomography_cmd ()
│ │ ├── tomography_flyscan_det ()
│ │ ├── tomography_flyscan_theta ()
│ │ ├── tomography_shutter ()
│ │ └── tomography_translation ()
│ ├── mc1_bragg
│ │ └── mc1_bragg ()
│ ├── mc2
│ │ │
│ │ ├── mc2_bragg ()
│ │ └── mc2_z ()
│ ├── mc2_bragg
│ │ └── mc2_bragg ()
│ ├── s1
│ │ │
│ │ ├── s1_bottom ()
│ │ ├── s1_in ()
│ │ ├── s1_out ()
│ │ ├── s1_t1 ()
│ │ ├── s1_t2 ()
│ │ ├── s1_top ()
│ │ ├── s1_xc ()
│ │ ├── s1_xs ()
│ │ ├── s1_yc ()
│ │ └── s1_ys ()
│ ├── s2
│ │ │
│ │ ├── s2_bottom ()
│ │ ├── s2_in ()
│ │ ├── s2_out ()
│ │ ├── s2_top ()
│ │ ├── s2_xc ()
│ │ ├── s2_xs ()
│ │ ├── s2_yc ()
│ │ └── s2_ys ()
│ ├── s3
│ │ │
│ │ ├── s3_bottom ()
│ │ ├── s3_in ()
│ │ ├── s3_out ()
│ │ ├── s3_top ()
│ │ ├── s3_xc ()
│ │ ├── s3_xs ()
│ │ ├── s3_y ()
│ │ ├── s3_yc ()
│ │ └── s3_ys ()
│ ├── ss1
│ │ │
│ │ ├── ss1_phi ()
│ │ ├── ss1_rx ()
│ │ ├── ss1_rz ()
│ │ ├── ss1_theta ()
│ │ ├── ss1_tx ()
│ │ ├── ss1_tz ()
│ │ ├── ss1_x ()
│ │ ├── ss1_y1 ()
│ │ ├── ss1_y2 ()
│ │ └── ss1_y3 ()
│ ├── ss2
│ │ │
│ │ ├── ss2_rx ()
│ │ ├── ss2_theta ()
│ │ ├── ss2_x ()
│ │ ├── ss2_y ()
│ │ └── ss2_z ()
│ ├── t3
│ │ │
│ │ ├── t3_m1y ()
│ │ ├── t3_m1z ()
│ │ ├── t3_m2y ()
│ │ ├── t3_m2z ()
│ │ ├── t3_m3rx ()
│ │ ├── t3_m3ry ()
│ │ ├── t3_m3rz ()
│ │ ├── t3_m3y ()
│ │ ├── t3_m3z ()
│ │ ├── t3_m4rx ()
│ │ ├── t3_m4ry ()
│ │ ├── t3_m4x ()
│ │ ├── t3_m4y ()
│ │ └── t3_x ()
│ └── t7
│ │
│ ├── t7_m1z ()
│ ├── t7_m2rx ()
│ ├── t7_m2ry ()
│ ├── t7_m2x ()
│ ├── t7_m2y ()
│ ├── t7_m2z ()
│ ├── t7_m3rx ()
│ ├── t7_m3ry ()
│ ├── t7_m3rz ()
│ ├── t7_m3z ()
│ ├── t7_x ()
│ └── t7_y ()
├── end_time (1,)
├── entry_identifier ()
├── experiment_identifier ()
├── flyScanDetector
│ │
│ ├── CaptureTime (1871,)
│ ├── data (1871, 2160, 2560)
│ ├── image_key (1871,)
│ └── zebraSM1 (1871,)
├── instrument
│ │
│ ├── flyScanDetector
│ │ │
│ │ ├── count_time (1871,)
│ │ ├── data (1871, 2160, 2560)
│ │ └── local_name ()
│ ├── image_key
│ │ └── image_key (1871,)
│ ├── name ()
│ ├── source
│ │ │
│ │ ├── current ()
│ │ ├── energy ()
│ │ ├── name ()
│ │ ├── probe ()
│ │ └── type ()
│ ├── zebraContinuousMoveController
│ │ └── CaptureTime (1871,)
│ └── zebraSM1
│ └── zebraSM1 (1871,)
├── program_name ()
├── scan_command ()
├── scan_dimensions (1,)
├── scan_identifier ()
├── start_time ()
├── title ()
├── tomo_entry
│ │
│ ├── control
│ │ └── data ()
│ ├── data
│ │ │
│ │ ├── data (1871, 2160, 2560)
│ │ └── rotation_angle (1871,)
│ ├── definition ()
│ ├── instrument
│ │ │
│ │ ├── detector
│ │ │ │
│ │ │ ├── data (1871, 2160, 2560)
│ │ │ ├── distance ()
│ │ │ ├── image_key (1871,)
│ │ │ ├── x_pixel_size ()
│ │ │ ├── x_rotation_axis_pixel_position ()
│ │ │ ├── y_pixel_size ()
│ │ │ └── y_rotation_axis_pixel_position ()
│ │ └── source
│ │ │
│ │ ├── current ()
│ │ ├── energy ()
│ │ ├── name ()
│ │ ├── probe ()
│ │ └── type ()
│ ├── sample
│ │ │
│ │ ├── rotation_angle (1871,)
│ │ ├── x_translation ()
│ │ ├── y_translation ()
│ │ └── z_translation ()
│ └── title ()
└── user01
└── username ()
PSI¶
The Tomcat beamline at the Swiss Light Source (SLS) at the Paul Scherrer Institut meta-data are reported below:
tomcat before 2017¶
Meta data name |
Value |
sample_name |
Blakely |
experimenter_name |
Federica Marone |
experimenter_affiliation |
Swiss Light Source |
experimenter_email |
|
instrument_name |
TOMCAT microCT |
source_name |
SLS |
source_beamline |
TOMCAT |
source_current |
401.096 |
source_current_unit |
mA |
sample_name |
/sls/X02DA/data/e11218/Data20/disk3/sample_name |
detector_name |
N/A |
objective_magnification |
10x |
scintillator_name |
LAG 20mu |
detector_exposure_time |
170 |
detector_exposure_time_unit |
ms |
monochromator_mono_stripe |
Ru/C |
monochromator_energy |
19.260 |
monochromator_energy_unit |
keV |
start_date |
2010-11-08T13:51:56Z |
number_of_projections |
1441 |
number_of_darks |
20 |
number_of_flats |
200 |
sample_in |
0 |
sample_in_unit |
deg |
sample_out |
3000 |
sample_out_unit |
deg |
start_angle |
0 |
start_angle_unit |
deg |
end_angle |
180 |
end_angle_unit |
deg |
angular_step |
0.125 |
angular_step_unit |
deg |
sample_x |
66.60 |
sample_y |
4382.00 |
sample_z |
5506.00 |
sample_xx |
-810.12 |
sample_zz |
1612.80 |
tomcat after 2017¶
{
"accessGroups": [
"slstomcat",
"p19555"
],
"classification": "IN=medium,AV=low,CO=low",
"contactEmail": "ElseMarie.Friis@nrm.se, peter.crane@yale.edu, krp@geo.au.dk",
"createdAt": "2023-03-02T16:19:26.096Z",
"createdBy": "slstomcat",
"creationTime": "2023-02-23T22:59:34.782Z",
"datasetName": "S266379\_10x\_",
"datasetlifecycle": {
"archivable": false,
"archiveRetentionTime": "2033-03-02T00:00:00.000Z",
"archiveStatusMessage": "datasetOnArchiveDisk",
"dateOfPublishing": "2026-03-02T00:00:00.000Z",
"isOnCentralDisk": true,
"publishable": false,
"publishedOn": "2023-07-10T14:14:21.940Z",
"retrievable": true,
"retrieveIntegrityCheck": false,
"retrieveStatusMessage": ""
},
"description": "SRXTM insights into major evolutionary transitions",
"history": [
{
"datasetlifecycle": {
"currentValue": {
"archivable": "false",
"archiveStatusMessage": "started",
"retrievable": "false"
},
"previousValue": {
"archivable": false,
"archiveRetentionTime": "2033-03-02T00:00:00.000Z",
"archiveStatusMessage": "scheduledForArchiving",
"dateOfPublishing": "2026-03-02T00:00:00.000Z",
"isOnCentralDisk": true,
"publishable": false,
"retrievable": false,
"retrieveIntegrityCheck": false,
"retrieveStatusMessage": ""
}
},
"id": "e8553257-c37c-4b39-922a-0c83a35c3c39",
"updatedAt": "2023-03-02T19:36:05.542Z",
"updatedBy": "archiveManager"
},
{
"datasetlifecycle": {
"currentValue": {
"archivable": "false",
"archiveStatusMessage": "datasetOnArchiveDisk",
"retrievable": "true"
},
"previousValue": {
"archivable": false,
"archiveRetentionTime": "2033-03-02T00:00:00.000Z",
"archiveStatusMessage": "started",
"dateOfPublishing": "2026-03-02T00:00:00.000Z",
"isOnCentralDisk": true,
"publishable": false,
"retrievable": false,
"retrieveIntegrityCheck": false,
"retrieveStatusMessage": ""
}
},
"id": "cb9a2fe8-009a-4088-81b4-755180088dd8",
"updatedAt": "2023-03-02T19:43:36.763Z",
"updatedBy": "archiveManager"
},
{
"datasetlifecycle": {
"currentValue": {
"publishedOn": "2023-07-10T14:14:21.940Z"
},
"previousValue": {
"archivable": false,
"archiveRetentionTime": "2033-03-02T00:00:00.000Z",
"archiveStatusMessage": "datasetOnArchiveDisk",
"dateOfPublishing": "2026-03-02T00:00:00.000Z",
"isOnCentralDisk": true,
"publishable": false,
"retrievable": true,
"retrieveIntegrityCheck": false,
"retrieveStatusMessage": ""
}
},
"id": "12fb47ee-5129-47e9-8540-daa925411764",
"isPublished": {
"currentValue": true,
"previousValue": false
},
"updatedAt": "2023-07-10T14:14:21.945Z",
"updatedBy": "anonymous"
}
],
"inputDatasets": [
"20.500.11935/9e9db9ec-413a-4dcf-8b43-bb6a7663a902"
],
"investigator": "ElseMarie.Friis@nrm.se, peter.crane@yale.edu, krp@geo.au.dk",
"isPublished": true,
"license": "CC BY-SA 4.0",
"numberOfFiles": 2161,
"numberOfFilesArchived": 2162,
"owner": "Else Marie Friis, Peter R. Crane, Kaj Raunsgaard Pedersen",
"ownerEmail": "ElseMarie.Friis@nrm.se, peter.crane@yale.edu, krp@geo.au.dk",
"ownerGroup": "p19555",
"packedSize": 5276518400,
"pid": "20.500.11935/c8fae0ad-270b-46d9-9daf-38fe625f4073",
"scientificMetadata": {
"beamlineParameters": {
"Beam energy": {
"u": "keV",
"unitSI": "(kg m^2) / s^2",
"v": 10,
"valueSI": 1.602176565e-15
},
"FE-Filter": "No Filter 100%",
"Monostripe": "Ru/C",
"OP-Filter1": "No Filter",
"OP-Filter2": "No Filter",
"OP-Filter3": "No Filter",
"Ring current": {
"u": "mA",
"unitSI": "A",
"v": 401.409,
"valueSI": 0.401409
}
},
"detectorParameters": {
"Actual pixel size": {
"u": "um",
"unitSI": "m",
"v": 0.65,
"valueSI": 6.5e-07
},
"Camera": "PCO.Edge 5.5",
"Delay time": {
"u": "ms",
"unitSI": "s",
"v": 0,
"valueSI": 0
},
"Exposure time": {
"u": "ms",
"unitSI": "s",
"v": 150,
"valueSI": 0.15
},
"Microscope": "Opt.Peter MB op",
"Microscope x position": {
"u": "mm",
"unitSI": "m",
"v": 138.26,
"valueSI": 0.13826
},
"Microscope y position": {
"u": "mm",
"unitSI": "m",
"v": -23.71,
"valueSI": -0.023710000000000002
},
"Microscope z position": {
"u": "mm",
"unitSI": "m",
"v": 52,
"valueSI": 0.052000000000000005
},
"Millisecond shutter": "not used",
"Objective": 10,
"Scintillator": "LuAg:Ce 20um (C20-76)",
"X-ROI End": 2560,
"X-ROI Start": 1,
"Y-ROI End": 2160,
"Y-ROI Start": 1
},
"postProcessingParameters": [
{
"commandLineArgument": {
"angle": "0",
"angleShift": 0,
"anglesFile": "",
"axisPositionIn2piScan": "",
"binSize": "1,1",
"centerOfRotation": "1231.2",
"corBandParams": "0.125,0.5,0.5,0.875",
"correctionOnly": false,
"correctionType": 7,
"createMissing": true,
"cutoff": "0.5",
"darkMedian": false,
"decompositionLevel": "0:0",
"differenceInStandardDeviation": 0,
"doFBPA": false,
"doNotCropReconstructions": false,
"doSimulateImages": false,
"doTestRun": false,
"filter": "parz",
"firstIndex": 1,
"flatMedian": false,
"geometry": "6",
"gridRecRoiParameters": "726,198,1838,2390",
"imageSize": "",
"inputSource": "/sls/X02DA/Data10/e19555/disk2/S266379_10x_/S266379_10x_.h5",
"inputType": "2",
"jsonFile": false,
"jsonMetaDataFile": "",
"keepSinograms": "0",
"logFile": "/sls/X02DA/data/e19555/Data10/disk2/S266379_10x_/S266379_10x_.log",
"maxRingWidth": 0,
"maxTif": "2.622e-03",
"mbaFilterParams": "",
"minTif": " -2.594e-03",
"moosmannFilterParams": "",
"numberOfGPUs": 0,
"pSWF_LUT_length": 0,
"paganinFilterParams": "",
"pathToPixelmaskFile": "",
"preFlatsOnly": false,
"prefix": "S266379_10x_",
"pswf": 0,
"recOnlySelect": "0,0",
"recOutputDir": "",
"reconstruct": "abs",
"ringRemoval": "0",
"roiParameters": "0,0,0,0",
"scaleImageFactor": 1,
"scanparameters": "1500,10,100,0,0",
"senderReceiverRatio": "8",
"separateAngles": "/sls/X02DA/data/e19555/Data10/disk2/S266379_10x_/S266379_10x_.h5",
"separateCorrection": "",
"shiftCorrection": false,
"sigmaInGaussFilter": "0",
"sinogramDirectory": "/sls/X02DA/Data10/e19555/disk2/S266379_10x_/sin",
"skipPiProj": true,
"stepLines": 1,
"stitching": "N",
"stripeOrientation": "v",
"stripeRemoval": "",
"thresholdInZinger": 0.95,
"tifConversionType": "8",
"underSampleSinoFactor": 1,
"verbose": 0,
"waveletPaddingMode": "0",
"waveletType": "0",
"widthOfSmoothingKernel": 9,
"zeroPadding": "0.5",
"zinger": ""
},
"gitRepositoryLink": "f9e3d5f356f014a4d55c53901f2ba9c5dbdea97e",
"postProcessingTimestamp": "2023-02-23T22:59:34.782Z"
}
],
"scanParameters": {
"Angular step": {
"u": "deg",
"unitSI": "rad",
"v": 0.12,
"valueSI": 0.0020943951023931952
},
"File Prefix": "S266379_10x_",
"Flat frequency": 0,
"Number of darks": 10,
"Number of flats": 100,
"Number of inter-flats": 0,
"Number of projections": 1500,
"Raw Source": "/sls/X02DA/Data10/e19555/disk2/S266379_10x_/",
"Rot Y max position": {
"u": "deg",
"unitSI": "rad",
"v": 180,
"valueSI": 3.141592653589793
},
"Rot Y min position": {
"u": "deg",
"unitSI": "rad",
"v": 0,
"valueSI": 0
},
"Rotation axis position": "Standard",
"Sample In": {
"u": "um",
"unitSI": "m",
"v": 0,
"valueSI": 0
},
"Sample Out": {
"u": "um",
"unitSI": "m",
"v": 5000,
"valueSI": 0.005
},
"Sample folder": "/sls/X02DA/data/e19555/Data10/disk2/S266379_10x_/",
"Sample holder X-position": {
"u": "um",
"unitSI": "m",
"v": 7835.4,
"valueSI": 0.0078354
},
"Sample holder Y-position": {
"u": "um",
"unitSI": "m",
"v": 2560.1,
"valueSI": 0.0025600999999999996
}
}
},
"size": 5272583164,
"sourceFolder": "/sls/X02DA/Data10/e19555/disk2/S266379_10x_/rec_8bit_abs",
"sourceFolderHost": "x02da-cons-bl-9.psi.ch",
"techniques": [],
"type": "derived",
"updatedAt": "2023-07-10T14:14:23.015Z",
"updatedBy": "anonymous",
"usedSoftware": [
"Schindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012), \"Fiji: an open-source platform for biological-image analysis\", Nature methods 9(7): 676-682, PMID 22743772, doi:10.1038/nmeth.2019",
"Marone, F. et al. (2017), \"Towards on-the-fly data post-processing for real-time tomographic imaging at TOMCAT\", Advanced Structural and Chemical Imaging 3(1): 1, doi:10.1186/s40679-016-0035-9"
],
"version": "3.1.0"
}