Wiki source code of Collection of HDF5 sample data from different beamlines
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1 | {{toc/}} | ||
2 | |||
3 | |||
4 | |||
5 | == how to find the public data in the [[gamma portal>>https://gamma-portal.desy.de/]] == | ||
6 | |||
7 | |||
8 | [[image:attach:image2023-9-28_16-42-5.png||height="250"]] | ||
9 | |||
10 | |||
11 | == How to look at the sample scripts ? == | ||
12 | |||
13 | for some Beamlines implemented an **online execution option** for the sample scripts | ||
14 | |||
15 | see the [[ Video how to use the tool>>https://syncandshare.desy.de/index.php/s/4qYwkWqQW2czj3x]] [[~[~[image:1726650353847-977.png~|~|height="137" width="290"~]~]>>https://syncandshare.desy.de/index.php/s/4qYwkWqQW2czj3x]] | ||
16 | |||
17 | and the link to the tool : [[https:~~/~~/max-sas.desy.de/>>url:https://max-sas.desy.de/]] | ||
18 | |||
19 | |||
20 | == FL21 == | ||
21 | |||
22 | === **Data: ** === | ||
23 | |||
24 | /asap3/flash/gpfs/fl21/2022/data/11015507/raw/hdf/offline/fl2user2~/~/FLASH2_USER2_stream_2_run41519_file1_20211019T152756.1 | ||
25 | |||
26 | === **analysis file **: === | ||
27 | |||
28 | /asap3/flash/gpfs/fl21/2022/data/11015507/processed/Example_analysis_THz_streaking_run41519.ipynb | ||
29 | |||
30 | {{view-file att--filename="Example_analysis_THz_streaking_run41519.pdf" display="thumbnail"/}} | ||
31 | |||
32 | === **description**: === | ||
33 | |||
34 | (% style="color:#333333" %)Experiment: THz streaking(%%) | ||
35 | (% style="color:#333333" %)Beamline: FL21(%%) | ||
36 | (% style="color:#333333" %)Instrument: THz streaking (%%) | ||
37 | (% style="color:#333333" %)Sample: Neon | ||
38 | |||
39 | The data was taken as part of the THz streaking photon diagnostic shifts. it contains GMD data and Time of Flight data ( recorded with the FLASH GHz ADCs) as well as beam arrival time (BAM) data. | ||
40 | |||
41 | we show how to read and interpolate the GMD data, look at the TOF data and sort a delay scan with the BAM | ||
42 | |||
43 | === **suggested reading:** === | ||
44 | |||
45 | (% style="color:#172b4d" %)R. Ivanov, (% class="nowrap" %)I. Bermúdez Macias(%%), (% class="nowrap" %)J. Liu(%%), (% class="nowrap" %)G. Brenner(%%), (% class="nowrap" %)J. Roensch-Schulenburg(%%), (% class="nowrap" %)G. Kurdi(%%), (% class="nowrap" %)U. Fruehling, K, Wenig(%%), (% class="nowrap" %)S Walther(%%), (% class="nowrap" %)A Dimitriou(% class="reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %), (% class="nowrap reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %)M Drescher(% class="reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %), (% class="nowrap reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %)I P Sazhina(% class="reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %), (% class="nowrap reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %)A K Kazansky(% class="reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %), (% class="nowrap reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %)N M Kabachnik(% class="reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %) and (% class="nowrap reveal-container reveal-content reveal-enabled reveal-no-animation reveal-plus-icon" %)S. Düsterer(%%) | ||
46 | (% style="text-align:left" %)//Single-shot temporal characterization of XUV pulses with duration from ~~10 fs to ~~350 fs at FLASH//(%%) | ||
47 | (% style="color:#172b4d" %)J. Phys. B: At. Mol. Opt. Phys. (2020)(%%) | ||
48 | (% class="Object" %)__[[https:~~/~~/doi.org/10.1088/1361-6455/ab9c38>>url:https://doi.org/10.1088/1361-6455/ab9c38||rel="nofollow" shape="rect" class="external-link"]]__ | ||
49 | |||
50 | Dennis Mayer, Fabiano Lever and Markus Gühr, ** ** | ||
51 | //Data analysis procedures for time-resolved x-ray photoelectron spectroscopy at a SASE free-electron-laser,// | ||
52 | Phys. B: At. Mol. Opt. Phys. **55**, 054002 (2022); [[https:~~/~~/doi.org/10.1088/1361-6455/ac3c91>>url:https://doi.org/10.1088/1361-6455/ac3c91||rel="nofollow" shape="rect" class="external-link"]] | ||
53 | |||
54 | |||
55 | == FL24 == | ||
56 | |||
57 | === **Data: ** === | ||
58 | |||
59 | /asap3/flash/gpfs/fl24/2023/data/11017906/raw/hdf/offline/fl2user1/ | ||
60 | |||
61 | |||
62 | === **analysis file **: === | ||
63 | |||
64 | asap3/flash/gpfs/fl24/2023/data/11017906/shared/data_loading.ipynb | ||
65 | |||
66 | {{view-file att--filename="data_loading.pdf" display="thumbnail"/}} | ||
67 | |||
68 | |||
69 | and other python files in this folder | ||
70 | |||
71 | === **description**: === | ||
72 | |||
73 | (% style="color:#333333" %)Experiment: Photoelectron spectroscopy(%%) | ||
74 | (% style="color:#333333" %)Beamline: FL24(%%) | ||
75 | (% style="color:#333333" %)Instrument: URSAPQ(%%) | ||
76 | (% style="color:#333333" %)Sample: ? | ||
77 | |||
78 | === **suggested reading:** === | ||
79 | |||
80 | Jan Metje, Fabiano Lever, Dennis Mayer, Richard James Squibb, Matthew S. Robinson, Mario Niebuhr, Raimund Feifel, Stefan Düsterer, Markus Gühr, | ||
81 | //URSA-PQ: A Mobile and Flexible Pump-Probe Instrument for Gas Phase Samples at the FLASH Free Electron Laser//, | ||
82 | Appl. Sci. **10**, 7882 (2020); [[http:~~/~~/dx.doi.org/10.3390/app10217882>>url:http://dx.doi.org/10.3390/app10217882||shape="rect" style="text-decoration: none;"]] | ||
83 | |||
84 | == PG1 == | ||
85 | |||
86 | === **Data:** === | ||
87 | |||
88 | /asap3/flash/gpfs/pg1/2023/data/11017909/raw/hdf/offline/fl1user3 | ||
89 | |||
90 | (% style="color:#333333" %)runs 43622 and 43624 (25 GB in total) | ||
91 | |||
92 | === **analysis file **: === | ||
93 | |||
94 | asap3/flash/gpfs/pg1/2023/data/11017909/processed/[[attach:PG1_data_analysis_Si_example_FAB.ipynb]] (version using the new FAB library) | ||
95 | |||
96 | |||
97 | asap3/flash/gpfs/pg1/2023/data/11017909/processed/previous_analysis/[[attach:PG1_data_analysis_Si_example.ipynb]] (version using the depreciated flashdaqhdfutils library ) | ||
98 | |||
99 | {{view-file att--filename="PG1_data_analysis_Si_example.pdf" display="thumbnail"/}} | ||
100 | |||
101 | === | ||
102 | (% style="color:#333333" %)** Description:**(%%) === | ||
103 | |||
104 | (% style="color:#333333" %) Experiment: time-resolved RIXS(%%) | ||
105 | (% style="color:#333333" %) Beamline: PG1(%%) | ||
106 | (% style="color:#333333" %) Instrument: TRIXS end station(%%) | ||
107 | (% style="color:#333333" %) Sample: Si(%%) | ||
108 | \\(% style="color:#333333" %) Sample was pumped with an optical laser and probed via soft X-ray RIXS by(%%) | ||
109 | (% style="color:#333333" %) varying the time delay between the optical laser and FEL.(%%) | ||
110 | (% style="color:#333333" %) Time delay was changed repeatedly from 2935 ps to 2939 ps (these are the delay(%%) | ||
111 | (% style="color:#333333" %) line encoder values of the optical laser ) in steps of 400fs, 1000 samples per(%%) | ||
112 | (% style="color:#333333" %) delay step.(%%) | ||
113 | \\(% style="color:#333333" %) RIXS images were collected via CCD camera (not full chip, only narrow region of(%%) | ||
114 | (% style="color:#333333" %) interest), operated in long exposure mode of 5 sec (integrating several FEL(%%) | ||
115 | (% style="color:#333333" %) trains per image).(%%) | ||
116 | |||
117 | |||
118 | === **suggested reading:** === | ||
119 | |||
120 | S. Dziarzhytski, M. Biednov, B. Dicke, A. Wang, P. S. Miedema, R. Y. Engel, J. O. Schunck, H. Redlin, H. Weigelt, F. Siewert, C. Behrens, M. Sinha, A. Schulte, B. Grimm-Lebsanft, S. G. Chiuzbăian, W. Wurth, M. Beye, M. Rübhausen, and G. Brenner, | ||
121 | //The TRIXS end-station for femtosecond time-resolved resonant inelastic x-ray scattering experiments at the soft x-ray free-electron laser FLASH//, | ||
122 | Struct. Dyn. **7**, 054301 (2020); [[https:~~/~~/doi.org/10.1063/4.0000029>>url:https://doi.org/10.1063/4.0000029||shape="rect" style="text-decoration: none;"]] | ||
123 | |||
124 | |||
125 | |||
126 | == PG2 / HEXTOF == | ||
127 | |||
128 | === **Data:** === | ||
129 | |||
130 | /asap3/flash/gpfs/pg2/2023/data/11019101/raw/hdf/offline/fl1user3/ | ||
131 | |||
132 | Runs for standard example of hextof workflow (from Spin-Gd/W(110) beamtime, ID 11013410): | ||
133 | |||
134 | * 44762 - chessy sample for PEEM mode calibration | ||
135 | * 44797 - energy calibration | ||
136 | * 44798 and 44799 - optical spot profile with two different fluences | ||
137 | * 44824, 44825, 44826 and 44827 - trMM data | ||
138 | |||
139 | (% style="color:#333333" %)(3.5 GB in total) | ||
140 | |||
141 | ===== **analysis file**: ===== | ||
142 | |||
143 | /asap3/flash/gpfs/pg2/2023/data/11019101/processed/4_hextof_workflow.ipynb | ||
144 | |||
145 | __ __ | ||
146 | |||
147 | Runs for example of BAM corrections (from H. Bentmann beamtime, ID 11013426): | ||
148 | |||
149 | * 44455 - energy calibration for W4f core level lines | ||
150 | * 44498 - trXPS dataset - t0 using side bands on W4f for BAM correction, alternative energy calibration method using SB and XPD normalization example | ||
151 | |||
152 | (0.9 GB in total) | ||
153 | |||
154 | ===== **analysis file**: ===== | ||
155 | |||
156 | /asap3/flash/gpfs/pg2/2023/data/11019101/processed/9_hextof_workflow_trXPD.ipynb - XPD normalization example | ||
157 | |||
158 | /asap3/flash/gpfs/pg2/2023/data/11019101/processed/10_hextof_workflow_trXPS_bam_correction.ipynb - BAM correction using SB | ||
159 | |||
160 | /asap3/flash/gpfs/pg2/2023/data/11019101/processed/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb -alternative energy calibration method using SB | ||
161 | |||
162 | |||
163 | === | ||
164 | (% style="color:#333333" %)** Description:**(%%) === | ||
165 | |||
166 | (% style="color:#333333" %) Experiment: time-resolved momentum microscopy(%%) | ||
167 | (% style="color:#333333" %) Beamline: PG2(%%) | ||
168 | (% style="color:#333333" %) Instrument: HEXTOF(%%) | ||
169 | (% style="color:#333333" %) Samples: Chessy and Gd/W(110)(%%) | ||
170 | |||
171 | |||
172 | Run 44762 was measured with a Hg lamp on the test "Chessy" sample to calibrate FoV in µm in the PEEM mode. | ||
173 | |||
174 | Runs 44798 and 44799 - optical spot profile measured in PEEM mode under the same settings as run 44762 | ||
175 | with two different attenuations of the pump laser to determine the spot size of the pump laser. | ||
176 | This is needed to estimate pump fluence during trMM runs (44824, 44825, 44826 and 44827) using values | ||
177 | of I,,0,, monitor of the pump laser. | ||
178 | |||
179 | Runs 44797 - measured with 36.2 eV in k-mode with manually variable sample bias from 28 to 32V by 1 V | ||
180 | every 2000 shots to calibrate the energy scale. | ||
181 | This energy calibration has to be used for trMM data. | ||
182 | |||
183 | Runs 44824, 44825, 44826 and 44827 were measured (% style="color:#333333" %)from Gd/W(110) sample which was pumped with | ||
184 | a 1030 nm s-polarized optical laser and probed with 36.2 eV for time-resolved momentum microscopy (trARPES) | ||
185 | varying the time delay between the optical laser and FEL. The time delay was changed in ZigZag manner repeatedly | ||
186 | from 1462.00 ps to 1464.85 ps with 200 steps and 1 sec waiting time at each step. | ||
187 | |||
188 | === **suggested reading:** === | ||
189 | |||
190 | 1. D. Kutnyakhov, R.P. Xian, M. Dendzik, M. Heber, F. Pressacco, S.Y. Agustsson, L. Wenthaus, H. Meyer, S. Gieschen, G. Mercurio, A. Benz, K. Bühlman, S. Däster, R. Gort, D. Curcio, K. Volckaert, M. Bianchi, Ch. Sanders, J A. Miwa, S. Ulstrup, A. Oelsner, C. Tusche, Y.-J. Chen, D. Vasilyev, K. Medjanik, G. Brenner, S. Dziarzhytski, H. Redlin, B. Manschwetus, S. Dong, J. Hauer, L. Rettig, F. Diekmann, K. Rossnagel, J. Demsar, H.-J. Elmers, Ph. Hofmann, R. Ernstorfer, G. Schönhense, Y. Acremann, and W. Wurth, | ||
191 | //Time- and momentum-resolved photoemission studies using time-of-flight momentum microscopy at a free-electron laser//, | ||
192 | Rev. Sci. Instrum. **91**, 013109 (2020); | ||
193 | [[https:~~/~~/doi.org/10.1063/1.5118777>>url:https://doi.org/10.1063/1.5118777||rel="nofollow" shape="rect" class="external-link"]] | ||
194 | 1. Single Event Data Frame Processor used as a backend to handle photoelectron resolved data streams | ||
195 | [[https:~~/~~/github.com/OpenCOMPES/sed>>url:https://github.com/OpenCOMPES/sed||shape="rect"]] | ||
196 | 1. Tutorial of typical data analysis workflow using sample data | ||
197 | [[https:~~/~~/opencompes.github.io/sed/tutorial/4_hextof_workflow.html#>>https://opencompes.github.io/sed/tutorial/4_hextof_workflow.html#]] |