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f | 1 | { | f | 1 | { |
2 | "author": "Becker, Moritz", | 2 | "author": "Becker, Moritz", | ||
3 | "author_email": "", | 3 | "author_email": "", | ||
4 | "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", | 4 | "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", | ||
5 | "doi": "10.35097/1433", | 5 | "doi": "10.35097/1433", | ||
6 | "doi_date_published": "2023", | 6 | "doi_date_published": "2023", | ||
7 | "doi_publisher": "", | 7 | "doi_publisher": "", | ||
8 | "doi_status": "True", | 8 | "doi_status": "True", | ||
9 | "groups": [], | 9 | "groups": [], | ||
10 | "id": "536ed090-94fb-4740-9583-0e5050e93c87", | 10 | "id": "536ed090-94fb-4740-9583-0e5050e93c87", | ||
11 | "isopen": false, | 11 | "isopen": false, | ||
12 | "license_id": "CC BY-SA 4.0 Attribution-ShareAlike", | 12 | "license_id": "CC BY-SA 4.0 Attribution-ShareAlike", | ||
13 | "license_title": "CC BY-SA 4.0 Attribution-ShareAlike", | 13 | "license_title": "CC BY-SA 4.0 Attribution-ShareAlike", | ||
14 | "metadata_created": "2023-08-04T08:50:47.728371", | 14 | "metadata_created": "2023-08-04T08:50:47.728371", | ||
t | 15 | "metadata_modified": "2023-08-04T08:52:04.171720", | t | 15 | "metadata_modified": "2023-08-04T08:53:36.971270", |
16 | "name": "rdr-doi-10-35097-1433", | 16 | "name": "rdr-doi-10-35097-1433", | ||
17 | "notes": "TechnicalRemarks: # RandomShimDB: A subset of the NMR | 17 | "notes": "TechnicalRemarks: # RandomShimDB: A subset of the NMR | ||
18 | magnet shimming database ShimDB\r\n\r\nRandomShimDB is a subset of the | 18 | magnet shimming database ShimDB\r\n\r\nRandomShimDB is a subset of the | ||
19 | NMR magnet shimming database | 19 | NMR magnet shimming database | ||
20 | [ShimDB](https://github.com/mobecks/ShimDB) and contains over 15000 | 20 | [ShimDB](https://github.com/mobecks/ShimDB) and contains over 15000 | ||
21 | instances. Data is aquired on a Spinsolve 80 Carbon spectrometer | 21 | instances. Data is aquired on a Spinsolve 80 Carbon spectrometer | ||
22 | (Magritek GmbH, Aachen, Germany, www.magritek.com) on 5%vv H2O in D2O | 22 | (Magritek GmbH, Aachen, Germany, www.magritek.com) on 5%vv H2O in D2O | ||
23 | and a water solution with CuSO4 (5mmol/L). \r\n\r\nRandomShimDB is | 23 | and a water solution with CuSO4 (5mmol/L). \r\n\r\nRandomShimDB is | ||
24 | part of \"Acquisitions with random shim values enhances AI-driven NMR | 24 | part of \"Acquisitions with random shim values enhances AI-driven NMR | ||
25 | shimming\" by M. Becker et al. [1].\r\n\r\nThe acquisition procedure | 25 | shimming\" by M. Becker et al. [1].\r\n\r\nThe acquisition procedure | ||
26 | was as follows. The manufacturer's automated shimming technique, based | 26 | was as follows. The manufacturer's automated shimming technique, based | ||
27 | on the downhill simplex method, was used to obtain a reference | 27 | on the downhill simplex method, was used to obtain a reference | ||
28 | spectrum. Then, the shims X, Y, Z and Z2 were varied. The dataset | 28 | spectrum. Then, the shims X, Y, Z and Z2 were varied. The dataset | ||
29 | parameters were obtained by relative offsets from the reference shim | 29 | parameters were obtained by relative offsets from the reference shim | ||
30 | values in a range R with weighting W, following Gaussian noise | 30 | values in a range R with weighting W, following Gaussian noise | ||
31 | sampling. For each combination, the raw FID, acquisition parameters, | 31 | sampling. For each combination, the raw FID, acquisition parameters, | ||
32 | and the shim values were stored. \r\n\r\n| Topic | | 32 | and the shim values were stored. \r\n\r\n| Topic | | ||
33 | Parameter | Value | 33 | Parameter | Value | ||
34 | ---------------------|------------------|-----------------------|\r\n| | 34 | ---------------------|------------------|-----------------------|\r\n| | ||
35 | Dataset parameters | Shims | X,Y,Z,Z2 | 35 | Dataset parameters | Shims | X,Y,Z,Z2 | ||
36 | |\r\n| | Weightings W | [1.2, 1.0, 2.0, | 36 | |\r\n| | Weightings W | [1.2, 1.0, 2.0, | ||
37 | 18.0] |\r\n| | Shim range R | +/- 50 | 37 | 18.0] |\r\n| | Shim range R | +/- 50 | ||
38 | |\r\n| | Sample I | H2O+CuSO4 | 38 | |\r\n| | Sample I | H2O+CuSO4 | ||
39 | |\r\n| | Sample II | 5vol% H2O in D2O | 39 | |\r\n| | Sample II | 5vol% H2O in D2O | ||
40 | |\r\n| | Nr. spectra | {5000,10000} | 40 | |\r\n| | Nr. spectra | {5000,10000} | ||
41 | |\r\n| Acquisition parameters | Nucleus | 1H | 41 | |\r\n| Acquisition parameters | Nucleus | 1H | ||
42 | |\r\n| | Bandwidth | 5 kHz | 42 | |\r\n| | Bandwidth | 5 kHz | ||
43 | |\r\n| | Points | 32768 | 43 | |\r\n| | Points | 32768 | ||
44 | |\r\n| | Repetition time | 2000 ms | 44 | |\r\n| | Repetition time | 2000 ms | ||
45 | |\r\n| | Phase correction | phi_0 | 45 | |\r\n| | Phase correction | phi_0 | ||
46 | | \r\n \r\n**We strongly encourage researchers to extend | 46 | | \r\n \r\n**We strongly encourage researchers to extend | ||
47 | ShimDB with their own subsets to stimulate developments. We offer to | 47 | ShimDB with their own subsets to stimulate developments. We offer to | ||
48 | include raw data or links to your publications into | 48 | include raw data or links to your publications into | ||
49 | ShimDB.**\r\n\r\n\r\n## Files format\r\n\r\nEach folder in | 49 | ShimDB.**\r\n\r\n\r\n## Files format\r\n\r\nEach folder in | ||
50 | RandomShimDB contains the following files: \r\n- data.1d -> the raw | 50 | RandomShimDB contains the following files: \r\n- data.1d -> the raw | ||
51 | FID.\r\n- shims.par -> Shim values, where only linear shims are | 51 | FID.\r\n- shims.par -> Shim values, where only linear shims are | ||
52 | non-zero.\r\n- acqu.par -> Acquisition parameters.\r\n- proc.par -> | 52 | non-zero.\r\n- acqu.par -> Acquisition parameters.\r\n- proc.par -> | ||
53 | Processing parameters.\r\n\r\nThe RandomShimDB root folder also | 53 | Processing parameters.\r\n\r\nThe RandomShimDB root folder also | ||
54 | contains the reference starting shims | 54 | contains the reference starting shims | ||
55 | (ReferenceShims.par).\r\n\r\n\r\n## Data loading\r\n\r\nWe deliver a | 55 | (ReferenceShims.par).\r\n\r\n\r\n## Data loading\r\n\r\nWe deliver a | ||
56 | python script ```utils_IO.py``` alongside | 56 | python script ```utils_IO.py``` alongside | ||
57 | [ShimDB](https://github.com/mobecks/ShimDB) to easily load the | 57 | [ShimDB](https://github.com/mobecks/ShimDB) to easily load the | ||
58 | database into numpy array structure using the [nmrglue | 58 | database into numpy array structure using the [nmrglue | ||
59 | packages](https://github.com/jjhelmus/nmrglue)[2].\r\n\r\nThe | 59 | packages](https://github.com/jjhelmus/nmrglue)[2].\r\n\r\nThe | ||
60 | following python libraries and packages are required: os, numpy, glob, | 60 | following python libraries and packages are required: os, numpy, glob, | ||
61 | nmrglue (>= v0.9.dev0)\r\n\r\n\r\n# References\r\n\r\n[1] M. Becker, | 61 | nmrglue (>= v0.9.dev0)\r\n\r\n\r\n# References\r\n\r\n[1] M. Becker, | ||
62 | S. Lehmkuhl, S. Kesselheim, J. G. Korvink, and M. Jouda, | 62 | S. Lehmkuhl, S. Kesselheim, J. G. Korvink, and M. Jouda, | ||
63 | \u201cAcquisitions with random shim values enhance AI-driven NMR | 63 | \u201cAcquisitions with random shim values enhance AI-driven NMR | ||
64 | shimming,\u201d J. Magn. Reson., p. 107323, 2022, doi: | 64 | shimming,\u201d J. Magn. Reson., p. 107323, 2022, doi: | ||
65 | https://doi.org/10.1016/j.jmr.2022.107323.\r\n\r\n[2] J. J. Helmus and | 65 | https://doi.org/10.1016/j.jmr.2022.107323.\r\n\r\n[2] J. J. Helmus and | ||
66 | C. P. Jaroniec, \u201cNmrglue: An open source Python package for the | 66 | C. P. Jaroniec, \u201cNmrglue: An open source Python package for the | ||
67 | analysis of multidimensional NMR data,\u201d J. Biomol. NMR, vol. 55, | 67 | analysis of multidimensional NMR data,\u201d J. Biomol. NMR, vol. 55, | ||
68 | no. 4, pp. 355\u2013367, 2013, doi: | 68 | no. 4, pp. 355\u2013367, 2013, doi: | ||
69 | https://doi.org/10.1007/s10858-013-9718-x.", | 69 | https://doi.org/10.1007/s10858-013-9718-x.", | ||
70 | "num_resources": 0, | 70 | "num_resources": 0, | ||
71 | "num_tags": 0, | 71 | "num_tags": 0, | ||
72 | "orcid": "0000-0002-0501-9849", | 72 | "orcid": "0000-0002-0501-9849", | ||
73 | "organization": { | 73 | "organization": { | ||
74 | "approval_status": "approved", | 74 | "approval_status": "approved", | ||
75 | "created": "2023-01-12T13:30:23.238233", | 75 | "created": "2023-01-12T13:30:23.238233", | ||
76 | "description": "RADAR (Research Data Repository) is a | 76 | "description": "RADAR (Research Data Repository) is a | ||
77 | cross-disciplinary repository for archiving and publishing research | 77 | cross-disciplinary repository for archiving and publishing research | ||
78 | data from completed scientific studies and projects. The focus is on | 78 | data from completed scientific studies and projects. The focus is on | ||
79 | research data from subjects that do not yet have their own | 79 | research data from subjects that do not yet have their own | ||
80 | discipline-specific infrastructures for research data management. ", | 80 | discipline-specific infrastructures for research data management. ", | ||
81 | "id": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | 81 | "id": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | ||
82 | "image_url": "radar-logo.svg", | 82 | "image_url": "radar-logo.svg", | ||
83 | "is_organization": true, | 83 | "is_organization": true, | ||
84 | "name": "radar", | 84 | "name": "radar", | ||
85 | "state": "active", | 85 | "state": "active", | ||
86 | "title": "RADAR", | 86 | "title": "RADAR", | ||
87 | "type": "organization" | 87 | "type": "organization" | ||
88 | }, | 88 | }, | ||
89 | "owner_org": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | 89 | "owner_org": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | ||
90 | "private": false, | 90 | "private": false, | ||
91 | "production_year": "2022", | 91 | "production_year": "2022", | ||
92 | "publication_year": "2023", | 92 | "publication_year": "2023", | ||
93 | "publishers": [ | 93 | "publishers": [ | ||
94 | { | 94 | { | ||
95 | "publisher": "Karlsruhe Institute of Technology" | 95 | "publisher": "Karlsruhe Institute of Technology" | ||
96 | } | 96 | } | ||
97 | ], | 97 | ], | ||
98 | "relationships_as_object": [], | 98 | "relationships_as_object": [], | ||
99 | "relationships_as_subject": [], | 99 | "relationships_as_subject": [], | ||
100 | "repository_name": "RADAR (Research Data Repository)", | 100 | "repository_name": "RADAR (Research Data Repository)", | ||
101 | "resources": [], | 101 | "resources": [], | ||
102 | "services_used_list": "", | 102 | "services_used_list": "", | ||
103 | "source_metadata_created": "2023", | 103 | "source_metadata_created": "2023", | ||
104 | "source_metadata_modified": "", | 104 | "source_metadata_modified": "", | ||
105 | "state": "active", | 105 | "state": "active", | ||
106 | "subject_areas": [ | 106 | "subject_areas": [ | ||
107 | { | 107 | { | ||
108 | "subject_area_additional": "", | 108 | "subject_area_additional": "", | ||
109 | "subject_area_name": "Engineering" | 109 | "subject_area_name": "Engineering" | ||
110 | } | 110 | } | ||
111 | ], | 111 | ], | ||
112 | "tags": [], | 112 | "tags": [], | ||
113 | "title": "Randomshimdb: a subset of the nmr magnet shimming database | 113 | "title": "Randomshimdb: a subset of the nmr magnet shimming database | ||
114 | shimdb", | 114 | shimdb", | ||
115 | "type": "vdataset", | 115 | "type": "vdataset", | ||
116 | "url": "https://doi.org/10.35097/1433" | 116 | "url": "https://doi.org/10.35097/1433" | ||
117 | } | 117 | } |