Commit 7af5b0e8 authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
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finished up from_dsc_info_to_ascii_file_vs_time

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"title": "Frequently Asked Questions",
"tags": [],
"description": "",
"content": " Before Your Venue Proposal How do I submit a proposal? To learn more about submitting a proposal for beam time, go to neutrons.ornl.gov/users. To submit your proposal, go to the proposal system. During your Experiment Where can I stay? A few options are available off-site and on-site. Check the neutron.ornl.gov users page for more infos.\n \nData Analysis I forgot my XCAMS password Simply go to How to reset password web page.\n How can I browse my data? Using ONCat, you will be able to view your data view the metadata and get infos about such or such data set find an experiment using keyword More features coming soon How can I get help analyzing my data? Just contact Jean Bilheux to discuss your needs.\nBy going over your experiment together, Jean will show you how to run the current tools and will develop customed python notebooks if needed.\n What are those \u0026#39;jupyter notebooks\u0026#39;? The jupyter notebook developed by jupyter are an easy way to run python code using only a browser. By accessing our analysis computer, you won\u0026rsquo;t have anythign to install. Refer to our How To page to learn how to do that.\n Where are my data and how can I access them? The following tutorial will show you where are you data and how you can access them. Just go to How To \u0026gt; Access your data\n I get a firefox error message when trying to start the jupyter notebooks on the analysis machine. After double clicking the start jupyter icon, I get an Firefox error message telling me that I have another Firefox window opened.\nThe short way to fix that is by starting the Help me application.\nThen go to the Desperate Actions\nand click the Fix Firefox!\nThis should fix your issue and you should be able to start the jupyter notebooks now.\n Where do I find ImageJ (or Fiji) on the analysis computer? Just follow the following path to find and start ImageJ. If you need to learn how to use ImageJ, check their tutorial web site\n How to cite our work? Use of CG1D beam line iMars3D iBeatles Metadata of the images and their meaning You can retrieve the metadata of your TIFF images using: ONCat the jupyter notebook list_tiff_metadata.ipynb. Check How To \u0026gt; Start the python notebooks \n Tag NameDescription ImageWidthThe number of columns in the image ImageHeightThe number of rows in the image BitsPerSampleThe number of bits per component (ie. 16-bits or 32-bits for each greyscale pixel in our case) SampleFormatSpecifies how to interpret each data sample in a pixel (1 = unsigned integer) SamplesPerPixelThe number of components per pixel (1 in our case, which is grey scale) Compression1 = None PhotometricInterpretation1 = Min is black MakeStrThe detector manufacture (eg. 'Andor' or 'SBIG') ModelStrThe detector model number SoftwareStrEPICS areaDetector \nTags 65000 to 650009 have no name and are used for timestamps and a unique ID\n Tag NameDescription 65000EPICS timestamp. The timestamp is made when the image is read out from the camera. Format is seconds.nanoseconds since Jan 1st 00:00 1990. 65001Unique ID for the image. Always 1 for single image acquisition, and incrementing up for camera and CT scans. Should always match the ImageCounter value. 65002EPICS timestamp (seconds part only) 65003EPICS timestamp (nanoseconds part only) Scan Information Tag NameDescription FileNameStrThe original file name part of the constructed file name (see below) InstrumentStr'CG1D' or 'VENUS' IPTSIPTS Number ITEMSITEMS Number SampleDescStrSample description (user entered) NotesStrUser notes DataSetStr'2D' or '3D' DataAcqModeStr'White Beam', 'TOF-cold/thermal', 'Epithermal' or 'Monochromatic' DataTypeStr'OB', 'Raw' or 'DF' Camera/Image Information Tag NameDescription ExposureTimeExposure time for the image (in seconds) ExposurePeriodExposure period for the image (Exposure Time + Readout Time in seconds). Not relevant for single image exposures. NumImages1= single image exposure (our normal mode of operation) ImageCounterAlways 1 for single image acquisition, and incrementing up for camera and CT scans. MinXMin X pixel (0 for full frame images) MinYMin Y pixel (0 for full frame images) SizeXSize of image in X dimension (should be equal to the ImageWidth value) SizeYSize of image in Y dimension (should be equal to the ImageLength value) TemperatureThe setpoint temperature (in C) TemperatureActualThe actual temperature read from the detector (in C) Motor Position \u0026amp; Scan Device Tag NameDescription MotScanDeviceStr'Small Rot' or 'Large Rot' used for this CT scan (if we are doing a camera scan or single image acquisition, this is not relevant) RotationActualActual position of the rotation stage used in the CT scan (or the previous scan if we are doing a camera scan or single image acquisition) MotRotTable.RBVLarge rotation table actual position MotRotTableLarge rotation table setpoint MotSmallRotTable.RBVSmall rotation table actual position MotSmallRotTableSmall rotation table setpoint MotLiftTable.RBVLift Table actual position MotLiftTableLift table setpoint MotShortAxis.RBVShort axis actual posiiton ... TIFF File Header Example TIFF Directory at offset 0x800008 (8388616) Image Width: 2048 Image Length: 2048 Bits/Sample: 16 Sample Format: unsigned integer Compression Scheme: None Photometric Interpretation: min-is-black Samples/Pixel: 1 Rows/Strip: 2048 Planar Configuration: single image plane Make: Unknown Model: Unknown Software: EPICS areaDetector Tag 65000: 837380408.136687 Tag 65001: 1 Tag 65002: 837380408 Tag 65003: 148080423 Tag 65010: FileNameStr:TiffHeaderTests Tag 65011: InstrumentStr:CG1D Tag 65012: IPTS:17255 Tag 65013: ITEMS:-1 Tag 65014: SampleDescStr:polarization test Tag 65015: NotesStr:polarization test Tag 65016: DataSetStr:2D Tag 65017: DataAcqModeStr:White Beam Tag 65018: DataTypeStr:Raw Tag 65019: ModelStr:DW936_BV Tag 65020: ManufacturerStr:Andor Tag 65021: ExposureTime:1.000000 Tag 65022: ExposurePeriod:5.451660 Tag 65023: NumExposures:1 Tag 65024: NumImages:1 Tag 65025: ImageCounter:1 Tag 65026: MinX:0 Tag 65027: MinY:0 Tag 65028: SizeX:2048 Tag 65029: SizeY:2048 Tag 65030: Temperature:-60.000000 Tag 65031: TemperatureActual:-57.830002 Tag 65032: MotScanDeviceStr:Small Rot Tag 65033: RotationActual:183.000132 Tag 65034: MotLiftTable.RBV:247.500452 Tag 65035: MotLiftTable:247.500452 Tag 65036: MotShortAxis.RBV:76.000000 Tag 65037: MotShortAxis:76.000000 Tag 65038: MotLongAxis.RBV:193.016000 Tag 65039: MotLongAxis:193.016000 Tag 65040: MotRotTable.RBV:182.996500 Tag 65041: MotRotTable:183.000000 Tag 65042: MotSmallRotTable.RBV:183.000132 Tag 65043: MotSmallRotTable:183.000000 Tag 65044: MotDetTable.RBV:200.000000 Tag 65045: MotDetTable:200.000000 Tag 65046: MotCameraVert.RBV:-51.699796 Tag 65047: MotCameraVert:-51.699796 Tag 65048: MotHoriTrans.RBV:28.000000 Tag 65049: MotHoriTrans:28.000000 Tag 65050: MotVertTrans.RBV:60.000000 Tag 65051: MotVertTrans:60.000000 Tag 65052: MotDiffuser.RBV:86.300000 Tag 65053: MotDiffuser:86.300000 Tag 65054: MotAperture.RBV:138.700000 Tag 65055: MotAperture:138.700000 Tag 65056: MotSlitVB.RBV:39.969938 Tag 65057: MotSlitVB:39.969938 Tag 65058: MotSlitVT.RBV:39.860484 Tag 65059: MotSlitVT:39.860484 Tag 65060: MotSlitHR.RBV:40.000000 Tag 65061: MotSlitHR:40.000000 Tag 65062: MotSlitHL.RBV:39.977781 Tag 65063: MotSlitHL:39.977781 Tag 65064: AndorCCDCooler:1 Tag 65065: AndorCCDTempStatusStr:Not stabilized at set point Tag 65066: AndorCCDPreAmpGain:0 Tag 65067: AndorCCDADCSpeed:2 \nWork With Us Visiting Researcher Program Link here\n Minority Serving Institutions Partnership Program Link here\n \n"
"content": " Before Your Venue Proposal How do I submit a proposal? To learn more about submitting a proposal for beam time, go to neutrons.ornl.gov/users. To submit your proposal, go to the proposal system. During your Experiment Where can I stay? A few options are available off-site and on-site. Check the neutron.ornl.gov users page for more infos.\n Data Analysis I forgot my XCAMS password Simply go to How to reset password web page.\n How can I browse my data? Using ONCat, you will be able to view your data view the metadata and get infos about such or such data set find an experiment using keyword More features coming soon How can I get help analyzing my data? Just contact Jean Bilheux to discuss your needs.\nBy going over your experiment together, Jean will show you how to run the current tools and will develop customed python notebooks if needed.\n What are those \u0026#39;jupyter notebooks\u0026#39;? The jupyter notebook developed by jupyter are an easy way to run python code using only a browser. By accessing our analysis computer, you won\u0026rsquo;t have anythign to install. Refer to our How To page to learn how to do that.\n Where are my data and how can I access them? The following tutorial will show you where are you data and how you can access them. Just go to How To \u0026gt; Access your data\n I get a firefox error message when trying to start the jupyter notebooks on the analysis machine. After double clicking the start jupyter icon, I get an Firefox error message telling me that I have another Firefox window opened.\nThe short way to fix that is by starting the Help me application.\nThen go to the Desperate Actions\nand click the Fix Firefox!\nThis should fix your issue and you should be able to start the jupyter notebooks now.\n Where do I find ImageJ (or Fiji) on the analysis computer? Just follow the following path to find and start ImageJ. If you need to learn how to use ImageJ, check their tutorial web site\n How to cite our work? Use of CG1D beam line iMars3D iBeatles Metadata of the images and their meaning You can retrieve the metadata of your TIFF images using: ONCat the jupyter notebook list_tiff_metadata.ipynb. Check How To \u0026gt; Start the python notebooks \n Tag NameDescription ImageWidthThe number of columns in the image ImageHeightThe number of rows in the image BitsPerSampleThe number of bits per component (ie. 16-bits or 32-bits for each greyscale pixel in our case) SampleFormatSpecifies how to interpret each data sample in a pixel (1 = unsigned integer) SamplesPerPixelThe number of components per pixel (1 in our case, which is grey scale) Compression1 = None PhotometricInterpretation1 = Min is black MakeStrThe detector manufacture (eg. 'Andor' or 'SBIG') ModelStrThe detector model number SoftwareStrEPICS areaDetector \nTags 65000 to 650009 have no name and are used for timestamps and a unique ID\n Tag NameDescription 65000EPICS timestamp. The timestamp is made when the image is read out from the camera. Format is seconds.nanoseconds since Jan 1st 00:00 1990. 65001Unique ID for the image. Always 1 for single image acquisition, and incrementing up for camera and CT scans. Should always match the ImageCounter value. 65002EPICS timestamp (seconds part only) 65003EPICS timestamp (nanoseconds part only) Scan Information Tag NameDescription FileNameStrThe original file name part of the constructed file name (see below) InstrumentStr'CG1D' or 'VENUS' IPTSIPTS Number ITEMSITEMS Number SampleDescStrSample description (user entered) NotesStrUser notes DataSetStr'2D' or '3D' DataAcqModeStr'White Beam', 'TOF-cold/thermal', 'Epithermal' or 'Monochromatic' DataTypeStr'OB', 'Raw' or 'DF' Camera/Image Information Tag NameDescription ExposureTimeExposure time for the image (in seconds) ExposurePeriodExposure period for the image (Exposure Time + Readout Time in seconds). Not relevant for single image exposures. NumImages1= single image exposure (our normal mode of operation) ImageCounterAlways 1 for single image acquisition, and incrementing up for camera and CT scans. MinXMin X pixel (0 for full frame images) MinYMin Y pixel (0 for full frame images) SizeXSize of image in X dimension (should be equal to the ImageWidth value) SizeYSize of image in Y dimension (should be equal to the ImageLength value) TemperatureThe setpoint temperature (in C) TemperatureActualThe actual temperature read from the detector (in C) Motor Position \u0026amp; Scan Device Tag NameDescription MotScanDeviceStr'Small Rot' or 'Large Rot' used for this CT scan (if we are doing a camera scan or single image acquisition, this is not relevant) RotationActualActual position of the rotation stage used in the CT scan (or the previous scan if we are doing a camera scan or single image acquisition) MotRotTable.RBVLarge rotation table actual position MotRotTableLarge rotation table setpoint MotSmallRotTable.RBVSmall rotation table actual position MotSmallRotTableSmall rotation table setpoint MotLiftTable.RBVLift Table actual position MotLiftTableLift table setpoint MotShortAxis.RBVShort axis actual posiiton ... TIFF File Header Example TIFF Directory at offset 0x800008 (8388616) Image Width: 2048 Image Length: 2048 Bits/Sample: 16 Sample Format: unsigned integer Compression Scheme: None Photometric Interpretation: min-is-black Samples/Pixel: 1 Rows/Strip: 2048 Planar Configuration: single image plane Make: Unknown Model: Unknown Software: EPICS areaDetector Tag 65000: 837380408.136687 Tag 65001: 1 Tag 65002: 837380408 Tag 65003: 148080423 Tag 65010: FileNameStr:TiffHeaderTests Tag 65011: InstrumentStr:CG1D Tag 65012: IPTS:17255 Tag 65013: ITEMS:-1 Tag 65014: SampleDescStr:polarization test Tag 65015: NotesStr:polarization test Tag 65016: DataSetStr:2D Tag 65017: DataAcqModeStr:White Beam Tag 65018: DataTypeStr:Raw Tag 65019: ModelStr:DW936_BV Tag 65020: ManufacturerStr:Andor Tag 65021: ExposureTime:1.000000 Tag 65022: ExposurePeriod:5.451660 Tag 65023: NumExposures:1 Tag 65024: NumImages:1 Tag 65025: ImageCounter:1 Tag 65026: MinX:0 Tag 65027: MinY:0 Tag 65028: SizeX:2048 Tag 65029: SizeY:2048 Tag 65030: Temperature:-60.000000 Tag 65031: TemperatureActual:-57.830002 Tag 65032: MotScanDeviceStr:Small Rot Tag 65033: RotationActual:183.000132 Tag 65034: MotLiftTable.RBV:247.500452 Tag 65035: MotLiftTable:247.500452 Tag 65036: MotShortAxis.RBV:76.000000 Tag 65037: MotShortAxis:76.000000 Tag 65038: MotLongAxis.RBV:193.016000 Tag 65039: MotLongAxis:193.016000 Tag 65040: MotRotTable.RBV:182.996500 Tag 65041: MotRotTable:183.000000 Tag 65042: MotSmallRotTable.RBV:183.000132 Tag 65043: MotSmallRotTable:183.000000 Tag 65044: MotDetTable.RBV:200.000000 Tag 65045: MotDetTable:200.000000 Tag 65046: MotCameraVert.RBV:-51.699796 Tag 65047: MotCameraVert:-51.699796 Tag 65048: MotHoriTrans.RBV:28.000000 Tag 65049: MotHoriTrans:28.000000 Tag 65050: MotVertTrans.RBV:60.000000 Tag 65051: MotVertTrans:60.000000 Tag 65052: MotDiffuser.RBV:86.300000 Tag 65053: MotDiffuser:86.300000 Tag 65054: MotAperture.RBV:138.700000 Tag 65055: MotAperture:138.700000 Tag 65056: MotSlitVB.RBV:39.969938 Tag 65057: MotSlitVB:39.969938 Tag 65058: MotSlitVT.RBV:39.860484 Tag 65059: MotSlitVT:39.860484 Tag 65060: MotSlitHR.RBV:40.000000 Tag 65061: MotSlitHR:40.000000 Tag 65062: MotSlitHL.RBV:39.977781 Tag 65063: MotSlitHL:39.977781 Tag 65064: AndorCCDCooler:1 Tag 65065: AndorCCDTempStatusStr:Not stabilized at set point Tag 65066: AndorCCDPreAmpGain:0 Tag 65067: AndorCCDADCSpeed:2 \nWork With Us Visiting Researcher Program Link here\n Minority Serving Institutions Partnership Program Link here\n \n"
},
{
"uri": "/tutorial/how_to_start_notebooks/",
......@@ -277,7 +277,7 @@
"title": "From .dsc Time Info to ASCII File vs Time",
"tags": [],
"description": "",
"content": " Notebook name: from_dsc_time_info_to_ascii_file_vs_time.ipynb\nDescription There are cases where you will need to use the metadata from the dsc file to retrieve the time information as the files themselves do not have this information any more (because they are not the original images anymore, because they have been moved, \u0026hellip;).\nSo this notebook will use the dsc files and match the time stamp information they contain with the base file name. Then will create an ascii file of the equivalent TIFF image vs time stamp\nINPUT\nfolder containing .dsc files\nOUTPUT\nfilename_vs_timestamp.txt\nsample_0000.tif 1045454545 sample_0001.tif 1045454546 sample_0002.tfi 1045454547 Instructions Select your IPTS Need help using the IPTS selector?\n Select the DSC Folder Using the folder selection tool, select the folder that contains the .dsc files.\nSelect the Image Folder Using the folder selection tool, select the folder that contains the images (TIFF or FITS) to match with the dsc files.\nSelect the Output Folder Using the folder selection tool, select the folder where the ascii file listing the image files and their time stamp will be created.\nAscii File Created Once you have selected the output folder, the ascii file will be automatically created and will look something like this\n"
"content": " Notebook name: from_dsc_time_info_to_ascii_file_vs_time.ipynb\nDescription There are cases where you will need to use the metadata from the dsc file to retrieve the time information as the files themselves do not have this information any more (because they are not the original images anymore, because they have been moved, \u0026hellip;).\nSo this notebook will use the dsc files and match the time stamp information they contain with the base file name. Then will create an ascii file of the equivalent TIFF image vs time stamp\nINPUT\nfolder containing .dsc files\nOUTPUT\nfilename_vs_timestamp.txt\nsample_0000.tif 1045454545 sample_0001.tif 1045454546 sample_0002.tfi 1045454547 Instructions Select your IPTS Need help using the IPTS selector?\n Select the DSC Folder Using the folder selection tool, select the folder that contains the .dsc files.\nSelect the Image Folder Using the folder selection tool, select the folder that contains the images (TIFF or FITS) to match with the dsc files.\nSelect the Output Folder Using the folder selection tool, select the folder where the ascii file listing the image files and their time stamp will be created.\nAscii File Created Once you have selected the output folder, the ascii file will be automatically created and will look something like this\nwhere the columns information are in order\n base file name time stamp (unix format) time stamp (user format) acquisition time (s) "
},
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......
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:root #header + #content > #left > #rlblock_left{
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......@@ -13,19 +13,19 @@
<title>Access :: Documentation for Hugo Learn Theme</title>
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......@@ -13,19 +13,19 @@
<title>Before your Arrival :: Documentation for Hugo Learn Theme</title>
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......@@ -2270,70 +2270,6 @@ and check out the items one by one.</p>
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......@@ -13,19 +13,19 @@
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