Commit 592d41d6 authored by Bilheux, Jean-Christophe's avatar Bilheux, Jean-Christophe
Browse files

removed documentation of notebooks not used anymore

parent ca331906
......@@ -3,7 +3,7 @@
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......@@ -613,32 +613,6 @@
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">
<a href="/tutorial/notebooks/calculate_water_intake_profile/">
- Calculate Water Intake <i class='fa fa-battery-empty'></i>
<i class="fa fa-check read-icon"></i>
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<li data-nav-id="/tutorial/notebooks/calibrated_transmission/" title="Calibrated Transmission" class="dd-item
......@@ -1709,13 +1683,7 @@
<a href='/'>Neutron Imaging</a> > Github Repositories
Github Repositories
</span>
......@@ -2684,22 +2652,6 @@ repositories hosting our programs</p>
......@@ -2755,20 +2707,20 @@ repositories hosting our programs</p>
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......@@ -613,32 +613,6 @@
<li data-nav-id="/tutorial/notebooks/calculate_water_intake_profile/" title="Calculate Water Intake" class="dd-item
">
<a href="/tutorial/notebooks/calculate_water_intake_profile/">
- Calculate Water Intake <i class='fa fa-battery-empty'></i>
<i class="fa fa-check read-icon"></i>
</a>
</li>
<li data-nav-id="/tutorial/notebooks/calibrated_transmission/" title="Calibrated Transmission" class="dd-item
......@@ -2672,22 +2646,6 @@ web site, and always <strong>welcome your comments</strong> to improve it (conta
......@@ -2743,20 +2701,20 @@ web site, and always <strong>welcome your comments</strong> to improve it (conta
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......
......@@ -60,7 +60,7 @@
"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 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"
"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"
},
{
"uri": "/tutorial/how_to_start_notebooks/",
......@@ -116,7 +116,7 @@
"title": "Notebooks Tutorials",
"tags": [],
"description": "",
"content": " bin_images bragg_edge_signal_vs_powder_peaks calculate_water_intake_profile calibrated_transmission combine_folders combine_images create_list_of_file_name_vs_time_stamp cylindrical_geometry_correction deal_images display_and_export_images_with_metadata_profile display_and_export_images_with_timestamp display_counts_of_region_vs_stack display_file_names_vs_time_stamp display_integrated_stack_of_images file_name_and_metadata_vs_time_stamp fix_images fix_images_with_negative_pixels frederick_ipts from_attenuation_to_concentration from_dsc_time_info_to_ascii_file_vs_time ipts_18813 gamma_filtering_tool images_metadata_matcher IN PROGRESS integrated_roi_counts_vs_file_name_and_time_stamp list_tiff_metadata metadata_ascii_parser metadata_overlapping_images normalization normalization_batch profile radial_profile registration rename_files resonance_imaging_experiment_vs_theory rotate_and_crop_images template_ui topaz_config_generator water_intake_profile_calculator \nTools File Selector Select IPTS \n Recently updated\n"
"content": " bin_images bragg_edge_signal_vs_powder_peaks calibrated_transmission combine_folders combine_images create_list_of_file_name_vs_time_stamp cylindrical_geometry_correction deal_images display_and_export_images_with_metadata_profile display_and_export_images_with_timestamp display_counts_of_region_vs_stack display_file_names_vs_time_stamp display_integrated_stack_of_images file_name_and_metadata_vs_time_stamp fix_images fix_images_with_negative_pixels frederick_ipts from_attenuation_to_concentration from_dsc_time_info_to_ascii_file_vs_time ipts_18813 gamma_filtering_tool images_metadata_matcher IN PROGRESS integrated_roi_counts_vs_file_name_and_time_stamp list_tiff_metadata metadata_ascii_parser metadata_overlapping_images normalization normalization_batch profile radial_profile registration rename_files resonance_imaging_experiment_vs_theory rotate_and_crop_images template_ui topaz_config_generator water_intake_profile_calculator \nTools File Selector Select IPTS \n Recently updated\n"
},
{
"uri": "/tutorial/how_to_start_amira/",
......@@ -153,13 +153,6 @@
"description": "",
"content": " Notebook name: bragg_edge_signal_vs_powder_peaks.ipynb\nDescription The main goal of this notebook is to display the ideal Bragg Edges of a list of elements and compare their signature to the signal of a set of FITS (MCP data) taken. Experimental set up can be changed by:\n distance source - detector detector time offset Start the notebook If you need help accessing this notebook, check the How To \u0026gt; Start the python notebooks tutorial.\nHow to Use It? Select your IPTS Check the full tutorial here\nSelect Working Folder Select the working folder using the file selector. If the time spectra file is part of the folder, it will be automatically loaded, if not, you will have the option to select the time spectra file next.\nCheck the file selection tool tutorial to learn how to use the file selector tool. Selection of Sample in the Image In order to calculate the signal of the loaded images, you must define the location of your sample in the image. But before doing so, the program will need to load a random subset of those images. You will need to define how many images you want to use to select that sample. A subset has been defined for you by default. Using this value (N), the program will load N images randomly choosen within the list of images in the working folder.\nRemember The more images you want to load, the longer it will take.\nOnce this subset has been defined, running the next cell will bring a user interface that will allow you to define the location(s) of your sample.\nSelect Powder Elements It\u0026rsquo;s now time to select the powder elements for which you want to see the Bragg Edges on top of your signal.\nDefine Experiment Setup This is where you can set up your experiment and play with these values to make sure the Bragg Edges of the reference powder elements show up at the right lambda in your signal data.\nDisplay Bragg Edges vs Signal Feel free to play with the iPlot widgets (above the plot) to zoom, pan, \u0026hellip; etc\n"
},
{
"uri": "/tutorial/notebooks/calculate_water_intake_profile/",
"title": "Calculate Water Intake",
"tags": [],
"description": "",
"content": "Notebook name: calculate_water_intake.ipynb\n"
},
{
"uri": "/tutorial/notebooks/calibrated_transmission/",
"title": "Calibrated Transmission",
......
......@@ -3,7 +3,7 @@
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