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UserData: Roi definition

Code Block

language	py
theme	RDark

def getROIs(run):
    """ Set parameter for ROI analysis. Set writeArea to True to write the full ROI in the h5 file.
    See roi_rebin.py for more info
    """
    if isinstance(run,str):
        run=int(run)
    ret_dict = {}
    if run<21:
        roi_dict = {}
        roi_dict['ROIs'] = [ [[1,2], [127,394], [655,923]]] # can define more than one ROI
        roi_dict['writeArea'] = True
        roi_dict['thresADU'] = None
        ret_dict['jungfrau1M'] = roi_dict
    elif run>20 and run<43:
        roi_dict = {}
        roi_dict['ROIs'] = [chip22] # can define more than one ROI
        roi_dict['writeArea'] = True
        roi_dict['thresADU'] = None
        ret_dict['jungfrau1M'] = roi_dict
    elif run>42:
        roi_dict = {}
        roi_dict['ROIs'] = [chip22] # can define more than one ROI
        roi_dict['writeArea'] = True
        roi_dict['thresADU'] = None
        ret_dict['jungfrau1M'] = roi_dict
    return ret_dict

Besides, the ROI definition, the parameters are the following:

writeArea: whether to write the full ROI to file or only the statistics (intensity sum, and other statistics)

thresADU: pixel intensity threshold. Any pixel below that value are set to 0.

Use of SmallDataAna_psana and extracting information from the average image

For the use of the interactive features of SmallDataAna_psana, we recommend to start it in an ipython session as interactive grabbing of user input is currently not implemented via the notebook. The first step is to create an average image that shows the feature of interest well.

From from smalldata_tools top level directory, run the following command to launch an IPython shell with pre-loaded a data analysis class for the relevant run

See the following link to learn how to start an interactive iPython session and make an average image for a given detector:

1.2 Area Detector treatment with DetObject#1.2AreaDetectortreatmentwithDetObject-InteractiveSmallDataAnasession

Once an average image has been created, a ROI can be selected by running:

Code Block

language	py
theme	RDark

Code Block

language	bash
theme	RDark

./producers/runSmallDataAna -r <#> [-e <expname>]

The average image can be then made by running

SDAna In: anaps.AvImage()

This will by default create an average image of 100 events of an area detector. The method will list and prompt for a detector name if more than one was recorded.
The full command with all its options can be looked via using the "?" feature of python:

SDAna In: anaps.AvImage?

More details can be found in the section Working with Images from camera/areadetectors

ROI

SDAna In: anaps.SelectRegion()

This will by draw the image and let you select a rectangular area of interest with the mouse. At this point, you click on two corners of the ROI. Once you are happy with your selection, it will print the numbers you need to enter in the producer file.

Below both what the terminal session looks like (here with an optional selection of different plot limits, by default 5% and 99.5% are used). Figure 2 will come up when you get asked if you are happy with the selection which appears on the right side of that figure. "n" means you can to click again until you are satisfied. "y" will print the ROI as it should be entered in the LittleDataProducer Smalldata producer file. Figure 3 shows A third figure will then show the ROI again, this time obtained from the raw data rather than the image (a technical detail). The more striking different is that the scaling/limit are now taken from only the ROI rather than the whole image.

Select ROI

The SelectRegion function works after an average image has been created. It expects you to select the two opposite corners of a rectangle. The selected region will then be plotted on the right hand side so that you can decide if this was good enough. If "yes" is selected, the ROI is plotted again using a color scale based on the ROI only and the ROI is printed in a form that can be copy/pasted into the producer python file.

Code Block

language	py
theme	RDark

SDana In [3]: anaps.SelectRegion(limits=[5,99.8])
plot AvImg_cs140_rob using the 5/99.8 percentiles as plot min/max: (1603.9, 1994.84)
Happy with this selection:
y
ROI: [[1,2], [55,76], [308,335]]

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Key

UserData: Roi definition

Use of SmallDataAna_psana and extracting information from the average image

Select ROI