x11ma/script/devices/eiger.py

from ijutils import *
from ch.psi.pshell.imaging.Overlays import *
from ch.psi.pshell.imaging.Utils import *
import ch.psi.pshell.imaging.Pen as Pen
import java.awt.Rectangle as Rectangle
import ch.psi.pshell.imaging.Data as Data
import ch.psi.pshell.device.Camera.DataType as DataType

eiger.setDataType(DataType.Float32)
eiger.getDataArray().monitored=True
###############################################################################
# ROI Integration
###############################################################################

def integrate_roi(source, x,y, w, h):
    if source.data is None:
        source.update()
    roi = source.data.getRoi(Rectangle(x,y, w, h))
    return roi.integrate(False)


class RoiIntensitySourceListener (ImageListener):
    def __init__(self, parent):
        self.parent = parent
    def onImage(self, origin, image, data):
        self.parent.update()
    def onError(self, origin, ex):
        pass
        

class RoiIntensity(ReadonlyRegisterBase):
    def __init__(self, name, source, x,y, w, h):
        ReadonlyRegisterBase.__init__(self, name)
        self.source=source
        self.roi = x,y, w, h
        self.source_listener = RoiIntensitySourceListener(self)
        
    def doRead(self):
        x,y, w, h = self.roi
        return integrate_roi(self.source, x,y, w, h)

    def doSetMonitored(self, value):
        if value:
            self.source.addListener(self.source_listener)
        else:
            self.source.removeListener(self.source_listener)

    def doClose(self):
         self.source.removeListener(self.source_listener)

def create_roi_devices(roi_list, add = True):  
    rois = []
    for r in roi_list:
        roi = RoiIntensity(r, image, roi_list[r][0], roi_list[r][1], roi_list[r][2], roi_list[r][3])
        if add:
            add_device(roi, True)
        rois.append(roi)
    return rois
    
###############################################################################
# Frame integration
###############################################################################
"""
def get_image(source, roi=None, wait_next=False):
    if wait_next:
        source.waitNext(-1)
    elif wait_next:
        if str(source.camera)=="Single":
            eiger.start()
            eiger.waitCacheChange(20000)
    ret = load_image(Utils.grayscale(source.output, Rectangle(roi[0], roi[1], roi[2], roi[3]) if (roi is not None) else None))
    return ret
    
def grab_frames(source, samples, roi=None, wait_next=False, sleep=0):
    frames = []            
    for i in range(samples):
        if sleep>0:
            time.sleep(sleep)
        aux = get_image(source, roi, wait_next)        
        frames.append(aux)        
    return frames
    
def average_frames(source, samples=1, roi=None, wait_next=False, sleep=0, as_float=True):
    return average_ips(grab_frames(source, samples, roi, wait_next, sleep), as_float)

def integrate_frames(source, samples=1, roi=None, wait_next=False, sleep=0, as_float=True):
    return integrate_ips(grab_frames(source, samples, roi, wait_next, sleep), as_float)
"""
def grab_frame(source, roi=None, wait_next=False, rmv_outliers=True):
    if wait_next:
        if str(eiger.grabMode)=="Single":
            eiger.start()
            #eigar.waitCacheChange(20000)
        source.waitNext(20000)
    #ret = load_image(Utils.grayscale(source.output, Rectangle(roi[0], roi[1], roi[2], roi[3]) if (roi is not None) else None))
    time.sleep(1.0)
    data=source.data
    if roi is not None:
        data = data.getRoi(Rectangle(roi[0], roi[1], roi[2], roi[3]))
    #ret = load_image(img)
    if rmv_outliers:
        #data = remove_outliers(data)
        data.threshold(1e9, False, None)
    return data
    
def grab_frames(source, samples, roi=None, wait_next=False, sleep=0, rmv_outliers=True):
    frames = []            
    for i in range(samples):
        if (i>0) and (sleep>0):
            time.sleep(sleep)
        aux = grab_frame(source, roi, wait_next, rmv_outliers)        
        frames.append(aux)        
    return frames
    
def integrate_frames(frames):
    if frames is None or (len(frames)==0):
        return None
    ret = frames[0].copy()
    for data in frames[1:]:
        ret.sum(data)
    return ret

def average_frames(frames):
    ret = integrate_frames(frames)
    if ret is not None:
        ret.div(len(frames))        
    return ret 

"""
def remove_outliers(imgdata, threshold = 1e9, replace_value=None):
    if replace_value is None:
        if str(imgdata.getType()) in  ('float', 'double'):
            replace_value = float('NaN')
        else:
            replace_value = 0
    data =  imgdata.copy()
    for i in range(data.width):        
        for j in range(data.height):
            if data.getElementDbl(j,i, False) >=threshold:
                data.setElement(j*data.width + i, replace_value)
    return data
"""

def save_as_tiff(data, filename, check=False, show = False):
    if type(data) == Data:
        ip = load_array(data.matrix)
    else:
        ip = data
        
    data = get_ip_array(ip)
    #ip.show()
    #plot(data)
    if not os.path.exists(os.path.dirname(filename)):
        os.makedirs(os.path.dirname(filename))    
    save_image(ip, filename,"tiff")    
    
    if check:
        import java.util.Arrays  as Arrays
        ip=open_image(filename)
        read = get_ip_array(ip)
        if not Arrays.deepEquals(read, data):
            raise Exception("Error reading array")
        #plot(read)

def trigger_eiger(wait=False):
    eiger.start()
    if wait:
        eiger.waitNewImage(20000)

        

if False:  
    integrate_roi(image, 10, 5, 20, 10)
            
    add_device(RoiIntensity("Region1", image, 10, 5, 20, 10), True)
    add_device(RoiIntensity("Region2", image, 10, 5, 40, 20), True)
    
    
    import ch.psi.pshell.data.ProviderCSV as ProviderCSV 
    ProviderCSV.setDefaultItemSeparator(" ")
    tscan((Region1, Region2), 10, 0.1, layout="table", provider = "csv")
    
    ret = grab_frames(image, 10, sleep=0.1)
    av = integrate_frames(ret)
    save_as_tiff(av,"{images}/data.tif", True)


    print "Success"