diff --git a/docs/JFJOCH_WRITER.md b/docs/JFJOCH_WRITER.md index 62a11945..9ffd2b64 100644 --- a/docs/JFJOCH_WRITER.md +++ b/docs/JFJOCH_WRITER.md @@ -147,41 +147,49 @@ For the time being it only works with Durin XDS plugin, and require DECTRIS Albu Data file has the following structure: -| Location | Description | Optional | Linked in master file v. 2 | -|--------------------------------------------------|---------------------------------------------------------------------------------------------------------------------|:--------:|:--------------------------:| -| /entry/data/data | Images | | X | -| /entry/detector/timestamp | Timestamp of the image | | | -| /entry/detector/exptime | Exposure time of the image | | | -| /entry/detector/number | Image number; if image rejection was used this will be the original image number | | | -| /entry/detector/det_info | Debug field of the JF detector | X | | -| /entry/detector/storage_cell_image | Storage cell number | X | X * | -| /entry/detector/rcv_delay | Receiver delay for the image (Jungfraujoch debugging) | X | | -| /entry/detector/rcv_free_send_buffers | Receiver number of free send buffers at the time of sending the image (Jungfraujoch debugging) | X | | -| /entry/detector/data_collection_efficiency_image | Ratio of received and expected UDP packets | X | X * | -| /entry/detector/packets_expected | Number of UDP packets expected for the image | X | | -| /entry/detector/packets_received | Number of UDP packets received for the image | X | | -| /entry/image/max_value | Max viable value of the image (excl. overloads, etc.) | X | | -| /entry/azint/bin_to_q | Azimuthal integration - bin-to-Q mapping | X | | -| /entry/azint/image | Azimuthal integration - per image | X | X | -| /entry/MX/peakXPosRaw | Peak position X (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | -| /entry/MX/peakYPosRaw | Peak position Y (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | -| /entry/MX/peakTotalIntensity | Peak total intensity (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | -| /entry/MX/nPeaks | Number of peaks per image (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | -| /entry/MX/strongPixels | Number of strong pixel per image | X | X | -| /entry/MX/nPeaksRingFiltered | Number of peaks not belonging to rings | X | X | -| /entry/MX/imageIndexed | Image is successfully indexed | X | X | -| /entry/MX/profileRadius | Crystal profile radius for indexed images | X | X | -| /entry/MX/latticeIndexed | Crystal lattice for the image, assuming it is indexed | X | X | -| /entry/MX/bkgEstimate | Mean value of pixels in the radius of 3-5 A | X | X | -| /entry/MX/resolutionEstimate | Resolution estimate based on on-the-fly integration | X | X | -| /entry/roi/{roi_name}/max | Max pixel value for roi named {roi_name} | X | X | -| /entry/roi/{roi_name}/sum | Sum pixel value for roi named {roi_name} | X | X | -| /entry/roi/{roi_name}/sum_sq | Sum pixel values squared for roi named {roi_name} | X | X | -| /entry/roi/{roi_name}/npixel | Number of valid pixel for roi named {roi_name} | X | X | -| /entry/roi/{roi_name}/x | Weighted X-coordinate for roi named {roi_name} | X | X | -| /entry/roi/{roi_name}/y | Weighted Y-coordinate for roi named {roi_name} | X | X | -| /entry/xfel/pulseID | Pulse ID (for XFEL only) | X | X | -| /entry/xfel/eventCode | Event code (for XFEL only) | X | X | +| Location | Description | Optional | Linked in master file v. 2 | +|--------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------:|:--------------------------:| +| /entry/data/data | Images | | X | +| /entry/detector/timestamp | Timestamp of the image | | | +| /entry/detector/exptime | Exposure time of the image | | | +| /entry/detector/number | Image number; if image rejection was used this will be the original image number | | | +| /entry/detector/det_info | Debug field of the JF detector | X | | +| /entry/detector/storage_cell_image | Storage cell number | X | X * | +| /entry/detector/rcv_delay | Receiver delay for the image (Jungfraujoch debugging) | X | | +| /entry/detector/rcv_free_send_buffers | Receiver number of free send buffers at the time of sending the image (Jungfraujoch debugging) | X | | +| /entry/detector/data_collection_efficiency_image | Ratio of received and expected UDP packets | X | X * | +| /entry/detector/packets_expected | Number of UDP packets expected for the image | X | | +| /entry/detector/packets_received | Number of UDP packets received for the image | X | | +| /entry/image/max_value | Max viable value of the image (excl. overloads, etc.) | X | | +| /entry/azint/bin_to_q | Azimuthal integration - bin-to-Q mapping | X | | +| /entry/azint/image | Azimuthal integration - per image | X | X | +| /entry/MX/peakXPosRaw | Peak position X (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/peakYPosRaw | Peak position Y (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/peakTotalIntensity | Peak total intensity (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/peakH | Miller index h for each detected (indexed) peak | X | X | +| /entry/MX/peakK | Miller index k for each detected (indexed) peak | X | X | +| /entry/MX/peakL | Miller index l for each detected (indexed) peak | X | X | +| /entry/MX/peakDistEwaldSphere | Distance of the peak from the Ewald sphere (prediction) | X | X | +| /entry/MX/nPeaks | Number of peaks per image (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/strongPixels | Number of strong pixel per image | X | X | +| /entry/MX/nPeaksRingFiltered | Number of peaks not belonging to rings | X | X | +| /entry/MX/imageIndexed | Image is successfully indexed | X | X | +| /entry/MX/profileRadius | Crystal profile radius for indexed images | X | X | +| /entry/MX/latticeIndexed | Crystal lattice for the image, assuming it is indexed | X | X | +| /entry/MX/bkgEstimate | Mean value of pixels in the radius of 3-5 A | X | X | +| /entry/MX/resolutionEstimate | Resolution estimate based on on-the-fly integration | X | X | +| /entry/MX/beam_corr_x | Beam center correction applied during processing (X) [pixel] | X | X | +| /entry/MX/beam_corr_y | Beam center correction applied during processing (Y) [pixel] | X | X | +| /entry/MX/niggli_class | Niggli class identifier of the indexed Bravais lattice (per image) - see [International Tables for Crystallography A (2016). Vol. A, Table 3.1.3.1](https://onlinelibrary.wiley.com/iucr/itc/Ac/ch3o1v0001/table3o1o3o1.pdf) | X | X | +| /entry/MX/bravais_lattice | Bravais lattice short code (per image), e.g., aP, mC, oF, tI, hP, hR, cF | X | X | +| /entry/roi/{roi_name}/max | Max pixel value for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/sum | Sum pixel value for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/sum_sq | Sum pixel values squared for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/npixel | Number of valid pixel for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/x | Weighted X-coordinate for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/y | Weighted Y-coordinate for roi named {roi_name} | X | X | +| /entry/xfel/pulseID | Pulse ID (for XFEL only) | X | X | +| /entry/xfel/eventCode | Event code (for XFEL only) | X | X | \* - Datasets from `/entry/detector` in data file are mapped to `/entry/instrument/detector/detectorSpecific` in master file.