AbstractXRFSpectrum.py

"""
Represents Abstract XRF spectrum (name could be discussed) Abstract class is 
compatible with queue_entry and emits these signals during the spectrum:
 - xrfSpectrumStarted  
 - xrfSpectrumFinished
 - xrfSpectrumFailed
 - xrfSpectrumStatusChanged  

Functions that needs a reimplementation:
- execute_spectrum_command : actual execution command
- cancel_spectrum
"""

import os
import logging
import time
import gevent
import numpy
import abc
from HardwareRepository.TaskUtils import cleanup	
from matplotlib.figure import Figure
from matplotlib.backends.backend_agg import FigureCanvasAgg


class AbstractXRFSpectrum(object, metaclass=abc.ABCMeta):
    """
    Descript. 
    """
    
    def __init__(self):
        """
        Descript. :
        """
        self.can_spectrum = None
        self.ready_event = None
        self.spectrum_info = None
        self.spectrum_data = None
        self.mca_calib = (10, 20, 0)
        self.spectrum_running = None

        self.energy_hwobj = None
        self.transmission_hwobj = None
        self.db_connection_hwobj = None
        self.beam_info_hwobj = None

        self.ready_event = gevent.event.Event()
 
        self.startXrfSpectrum = self.start_spectrum

    def start_spectrum(self, ct, spectrum_directory, archive_directory, prefix,
            session_id=None, blsample_id=None, adjust_transmission=True):
        """
        Descript. :
        """
        if not self.can_spectrum:
            self.spectrum_command_aborted()
            return False

        self.spectrum_info = {"sessionId": session_id, "blSampleId": blsample_id}
        if not os.path.isdir(archive_directory):
            logging.getLogger().debug("XRFSpectrum: creating directory %s" % archive_directory)
            try:
                if not os.path.exists(archive_directory):
                    os.makedirs(archive_directory)
                if not os.path.exists(spectrum_directory):
                    os.makedirs(spectrum_directory)
            except OSError as diag:
                logging.getLogger().error(\
                    "XRFSpectrum: error creating directory %s (%s)" % \
                    (archive_directory, str(diag)))
                self.emit('xrfSpectrumStatusChanged', ("Error creating directory", ))
                self.spectrum_command_aborted()
                return False

        archive_file_template = os.path.join(archive_directory, prefix)
        spectrum_file_template = os.path.join(spectrum_directory, prefix)
        if os.path.exists(archive_file_template + ".dat"):
            i = 1
            while os.path.exists(archive_file_template + "%d.dat" %i):
                  i = i + 1
            archive_file_template += "_%d" % i
            spectrum_file_template += "_%d" % i
            prefix += "_%d" % i

        spectrum_file_dat_filename = os.path.extsep.join((spectrum_file_template, "dat"))
        archive_file_dat_filename = os.path.extsep.join((archive_file_template, "dat"))
        archive_file_png_filename = os.path.extsep.join((archive_file_template, "png"))
        archive_file_html_filename = os.path.extsep.join((archive_file_template, "html"))

        self.spectrum_info["filename"] = prefix
        self.spectrum_info["scanFilePath"] = spectrum_file_dat_filename
        self.spectrum_info["scanFileFullPath"] = archive_file_dat_filename
        self.spectrum_info["jpegScanFileFullPath"] = archive_file_png_filename
        self.spectrum_info["exposureTime"] = ct
        self.spectrum_info["annotatedPymcaXfeSpectrum"] = archive_file_html_filename
        self.spectrum_info["htmldir"] = archive_directory
        self.spectrum_command_started()
        logging.getLogger().debug("XRFSpectrum: spectrum dat file is %s", spectrum_file_dat_filename)
        logging.getLogger().debug("XRFSpectrum: archive file is %s", archive_file_dat_filename)

        self.execute_spectrum_command(ct, spectrum_file_dat_filename, adjust_transmission)
       
    def execute_spectrum_command(self, count_time, filename, adjust_transmission=True):    
        """
        Descript. :
        """
        pass
   
    def cancel_spectrum(self, *args):
        """
        Descript. :
        """
        pass

    def spectrum_command_ready(self):
        """
        Descript. :
        """
        if not self.spectrum_running:
            self.emit('xrfSpectrumReady', (True, ))

    def spectrum_command_not_ready(self):
        """
        Descript. :
        """
        if not self.spectrum_running:
            self.emit('xrfSpectrumReady', (False, ))

    def spectrum_command_started(self, *args):
        """
        Descript. :
        """
        self.spectrum_info['startTime'] = time.strftime("%Y-%m-%d %H:%M:%S")
        self.spectrum_running = True
        self.emit('xrfSpectrumStarted', ())

    def spectrum_command_failed(self, *args):
        """
        Descript. :
        """
        self.spectrum_info['endTime'] = time.strftime("%Y-%m-%d %H:%M:%S")
        self.spectrum_running = False
        self.store_xrf_spectrum()
        self.emit('xrfSpectrumFailed', ())
        self.ready_event.set()
    
    def spectrum_command_aborted(self, *args):
        """
        Descript. :
        """
        self.spectrum_running = False
        self.emit('xrfSpectrumFailed', ())
        self.ready_event.set()

    def spectrum_command_finished(self):
        """
        Descript. :
        """
        with cleanup(self.ready_event.set):
            self.spectrum_info['endTime'] = time.strftime("%Y-%m-%d %H:%M:%S")
            self.spectrum_running = False

            xmin = 0
            xmax = 0
            mca_data = []
            calibrated_data = []

            try:
               spectrum_file_raw = open(self.spectrum_info["scanFileFullPath"], "w")
               archive_file_raw = open(self.spectrum_info["scanFilePath"], "w")
            except:
               logging.getLogger("HWR").exception(
                 "XRFSpectrum: could not create spectrum result raw file %s" % \
                 self.spectrum_info["scanFileFullPath"])

            for n, value in enumerate(self.spectrum_data):
                energy = (self.mca_calib[2] + \
                          self.mca_calib[1] * n + \
                          self.mca_calib[0] * n * n) / 1000
                if energy < 13:
                    if energy > xmax:
                        xmax = value
                    if energy < xmin:
                        xmin = value
                    calibrated_data.append([energy, value])
                    mca_data.append((n / 1000.0, value))
                    if spectrum_file_raw:
                        spectrum_file_raw.write("%f,%f\r\n" % (energy, value))
                    if archive_file_raw:
                        archive_file_raw.write("%f,%f\r\n" % (energy, value))
            if spectrum_file_raw:
                spectrum_file_raw.close()
            if archive_file_raw:
                archive_file_raw.close()

            calibrated_array = numpy.array(calibrated_data)

            self.spectrum_info["beamTransmission"] = self.transmission_hwobj.getAttFactor()
            self.spectrum_info["energy"] = self.get_current_energy()
            beam_size = self.beam_info_hwobj.get_beam_size()
            self.spectrum_info["beamSizeHorizontal"] = int(beam_size[0] * 1000)
            self.spectrum_info["beamSizeVertical"] = int(beam_size[1] * 1000)

            mca_config = {}
            mca_config["legend"] = self.spectrum_info["filename"]
            mca_config["file"] = self.config_filename
            mca_config["min"] = xmin
            mca_config["max"] = xmax
            mca_config["htmldir"] = self.spectrum_info["htmldir"]
            self.spectrum_info.pop("htmldir")
            self.spectrum_info.pop("scanFilePath")

            fig = Figure(figsize=(15, 11))
            ax = fig.add_subplot(111)
            ax.set_title(self.spectrum_info["jpegScanFileFullPath"])
            ax.grid(True)

            ax.plot(*(list(zip(*calibrated_array))), **{"color" : 'black'})
            ax.set_xlabel("Energy")
            ax.set_ylabel("Counts")
            canvas = FigureCanvasAgg(fig)
            logging.getLogger().info("XRFSpectrum: Rendering spectrum to PNG file : %s", \
                                     self.spectrum_info["jpegScanFileFullPath"])
            canvas.print_figure(self.spectrum_info["jpegScanFileFullPath"], dpi = 80)
            #logging.getLogger().debug("Copying .fit file to: %s", a_dir)
            #tmpname=filename.split(".")
            #logging.getLogger().debug("finished %r", self.spectrum_info)
            self.store_xrf_spectrum()
            self.emit('xrfSpectrumFinished', (mca_data, self.mca_calib, mca_config))
            
    def spectrum_status_changed(self, status):
        """
        Descript. :
        """
        self.emit('xrfSpectrumtatusChanged', (status, ))

    def store_xrf_spectrum(self):
        """
        Descript. :
        """
        logging.getLogger().debug("XRFSpectrum info %r", self.spectrum_info)
        if self.db_connection_hwobj:
            try:
                session_id = int(self.spectrum_info['sessionId'])
            except:
                return
            blsampleid = self.spectrum_info['blSampleId']
            self.db_connection_hwobj.storeXfeSpectrum(self.spectrum_info)

    def get_current_energy(self):
        """
        Descript. :
        """
        if self.energy_hwobj is not None:
            try:
                return self.energy_hwobj.getCurrentEnergy()
            except:
                logging.getLogger("HWR").exception("XRFSpectrum: couldn't read energy")