Tools2D

Data reduction of two-dimensional images in HDF5 (Dectris and various ESRF flavours) or EDF format. Routines for data conversion are available.

Features:

• Conversion from EDF to HDF5
• Conversion from HDF5 to EDF
• NOTE: it is possible to create in this way multi-edf files. It is however currently not foreseen to create multi HDF5 files.
• Averaging, subtraction and division of each two files using saxs programs is foreseen, as well.

Specific Features:

Two different data reduction routines exist:

EDF REDUCTION

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• This routine is based on spd / saxs programs.
• Normalization, azimuthal regrouping and output of ASCII files can be selected individually.
• Input format can be EDF or HDF5.
• An approximated variance calculation can be activated.
• The mask information is either taken from a header key ('default') or by a file selection in S2. In any case the mask file must be present in the working directory.
• The integration range can be restricted.
• Incase of problems, error output is available in the (minimized) terminal window of SAXSutilities2.

Typical application: partial azimuthal integration in a reduced angular range

NOTE: This can be also applied to files from the HDF5 REDUCTION pipeline !!

starting from normalized data ('norm')

• Select normalized images in Selection S1.
• Make sure that 'regrouping', 'output ASCII' and 'restrict integration' are all checked.
• Make sure the mask file is present in the working directory. The correct mask file is most of the time determined automatically ('apply mask' checked; 'default' selected).
• Choose if you want to calculate (A) I(q) averaged in a certain angular range or (B) I(angle) averaged in a certain q range.
• In case of (A): specify angular range. Negative angles are possible [-5 , 5]deg.
• In case of (B): specify q range in pixel coordinates (use plot2D with array coordinate system for selection).
• Click 'start data reduction'.

starting from azimuthally regrouped data ('azim' or 'ang')

• Select azimuthally regrouped images in Selection S1.
• Make sure that 'regrouping' is not checked, 'output ASCII' and 'restrict integration' must be checked.
• No mask file is necessary in this case.
• Choose if you want to calculate (A) I(q) averaged in a certain angular range or (B) I(angle) averaged in a certain q range.
• In case of (A): specify angular range. Negative angles are possible [-5 , 5]deg.
• In case of (B): specify q range in pixel coordinates (use plot2D with array coordinate system for selection).
• Click 'start data reduction'.
  
  

HDF5 REDUCTION

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• This routine is based on dahu / PyFAI
• Data reduction starts always from RAW data. Raw, dark (if applicable) and so called 'scaler' files (metadata!) must be available in the current working directory.
• The only input format is ESRF Lima style HDF5.
• Variance calculation is provided.
• Integration is curently done over the full azimuthal range.
• Data reduction is started by input files containing a JSON string.

Types of input files (for selection S1):

1. *_id02.singledetector.inp: File created during experiment.
2. *_norm.h5: Reduced data file has history information saved.
3. *_raw.h5: Raw data file

In case (1) and (2):

• The original correction parameters can be retrieved automatically and displayed (optionally) by clicking 'show parameters (for first selected file only).
• Parameters can be corrected (i.e. overwritten) by checking one of the available boxes.
• Non-checked values are taken from the input file.
• The name of the file to be reduced is also known from the input file
• Checking either of mask, distortion , flat or dark filename and leaving the field empty, disables the corresponding correction.
• Giving a number for dark_filename, subtracts a constant.

In case (3):

• Metadata are collected from the header (pixel size, center, wavelength distance, scaling factor) and can be overwritten with the static value, if checked.
• The name of the file to be reduced is defined in selection box S1.
• Mask, distortion, flat and dark image names are also taken from the image header, but can be overwritten with a static value (and checking the according box).
• ATTENTION: use the three check boxes marked with (III) to define if you want to do the correction or not.

Typical application of DAHU correction:

You are most probably concerned by case (3).

1. Select the Raw images which need to be corrected in selection S1.
2. Decide, if you need to correct metadata (e.g. in case you want to correct center coordinates, check the box in front of 'Center_1' and 'Center_2' and provide the correct values; in case you want to update the mask file, put the cross in front of regrouping_mask_filename and provide a filename).
3. Decide which corrections need to be done (distortion, flat, dark?) and check accordingly the boxes marked with (III).
4. 'run DAHU'.

Make sure that required files (mask, dark images) are available in the specified path (mask) or current working directory (dark).