# This file is part of Pymepix
#
# In all scientific work using Pymepix, please reference it as
#
# A. F. Al-Refaie, M. Johny, J. Correa, D. Pennicard, P. Svihra, A. Nomerotski, S. Trippel, and J. Küpper:
# "PymePix: a python library for SPIDR readout of Timepix3", J. Inst. 14, P10003 (2019)
# https://doi.org/10.1088/1748-0221/14/10/P10003
# https://arxiv.org/abs/1905.07999
#
# Pymepix is free software: you can redistribute it and/or modify it under the terms of the GNU
# General Public License as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with this program. If not,
# see <https://www.gnu.org/licenses/>.
import xml.etree.ElementTree as et
import zipfile
import os
import tempfile
import numpy as np
from pymepix.core.log import Logger
from .timepixconfig import TimepixConfig
[docs]class SophyConfig(TimepixConfig, Logger):
"""This class provides functionality for interpreting a .spx config file from SoPhy."""
def __init__(self, filename):
Logger.__init__(self, SophyConfig.__name__)
self.__filename = filename
self._dac_codes = {
"Ibias_Preamp_ON": 1,
"Ibias_Preamp_OFF": 2,
"VPreamp_NCAS": 3,
"Ibias_Ikrum": 4,
"Vfbk": 5,
"Vthreshold_fine": 6,
"Vthreshold_coarse": 7,
"Ibias_DiscS1_ON": 8,
"Ibias_DiscS1_OFF": 9,
"Ibias_DiscS2_ON": 10,
"Ibias_DiscS2_OFF": 11,
"Ibias_PixelDAC": 12,
"Ibias_TPbufferIn": 13,
"Ibias_TPbufferOut": 14,
"VTP_coarse": 15,
"VTP_fine": 16,
"Ibias_CP_PLL": 17,
"PLL_Vcntrl": 18,
}
self._dac_values = {
"Ibias_Preamp_ON": 128,
"Ibias_Preamp_OFF": 8,
"VPreamp_NCAS": 128,
"Ibias_Ikrum": 10,
"Vfbk": 128,
"Vthreshold_fine": 150,
"Vthreshold_coarse": 6,
"Ibias_DiscS1_ON": 128,
"Ibias_DiscS1_OFF": 8,
"Ibias_DiscS2_ON": 128,
"Ibias_DiscS2_OFF": 8,
"Ibias_PixelDAC": 150,
"Ibias_TPbufferIn": 128,
"Ibias_TPbufferOut": 128,
"VTP_coarse": 128,
"VTP_fine": 256,
"Ibias_CP_PLL": 128,
"PLL_Vcntrl": 128,
}
self.loadFile(self.__filename)
[docs] def loadFile(self, filename):
spx = zipfile.ZipFile(filename)
names = spx.namelist()
xml_string = spx.read(names[0])
self.parseDAC(xml_string)
self.parsePixelConfig(spx, names[-3:])
[docs] def saveMask(self):
old_file = zipfile.ZipFile(self.__filename, mode='r')
names = old_file.namelist()
mask_filename = names[-3]
buffer = old_file.read(mask_filename)
buffer_header = buffer[:27]
new_buffer = buffer_header + SophyConfig.__transform_to_bytes(self._mask)
SophyConfig.__replace_in_zip(self.__filename, mask_filename, new_buffer)
@staticmethod
def __transform_to_bytes(mask):
return mask.copy().transpose().flatten().tobytes()
@staticmethod
def __transform_from_bytes(bytes):
return np.frombuffer(bytes, dtype=np.int16).reshape(256, 256).transpose().copy()
@staticmethod
def __replace_in_zip(zip_filename, filename_to_replace, data_to_replace):
tmpfd, tmpname = tempfile.mkstemp(dir=os.path.dirname(zip_filename))
os.close(tmpfd)
with zipfile.ZipFile(zip_filename, mode='r') as zin:
with zipfile.ZipFile(tmpname, mode='w') as zout:
for name in zin.namelist():
if name != filename_to_replace:
zout.writestr(name, zin.read(name))
else:
zout.writestr(filename_to_replace, data_to_replace)
# replace with the temp archive
os.remove(zip_filename)
os.rename(tmpname, zip_filename)
[docs] def parseDAC(self, xmlstring):
"""Reads and formats DAC parameters"""
root = et.fromstring(xmlstring)
dac_setting = root.findall(
".//entry[@class='sophy.medipix.SPMPXDACCollection']"
)
dac_setting = dac_setting[0][0]
for element in dac_setting.findall(".//element[@class='java.util.Map.Entry']"):
key = element.find("key")
entry = element.find("entry")
data = entry.find("data")
dac_key = key.items()[-1][-1]
dac_value = int(data.items()[-1][-1])
self._dac_values[dac_key] = dac_value
self.debug(f"DAC Codes: {type(self.dacCodes())} \n{self.dacCodes()}")
[docs] def dacCodes(self):
"""Accessor for the dac parameters
Returns
----------
:obj:`list` of :obj:`tuples` (<dac code>, <value>)
The value for every DAC parameter"""
dac_codes = []
for key, value in self._dac_values.items():
code = self._dac_codes[key]
dac_codes.append((code, value))
return dac_codes
[docs] def biasVoltage(self):
pass
def _reverseBits(self, num):
bitsize = 4
binary = bin(num)
reverse = binary[-1:1:-1]
reverse = reverse + (bitsize - len(reverse)) * "0"
return int(reverse, 2)
[docs] def parsePixelConfig(self, zip_file, file_names):
"""Reads and formats the pixel data from config file.
Notes
----------
The spx config file saves the pixel information row by row while
the timepix camera expects the information column wise."""
buffer = zip_file.read(file_names[0])
self._mask = SophyConfig.__transform_from_bytes(buffer[27:])
buffer = zip_file.read(file_names[1])
self._test = np.fliplr(
np.frombuffer(buffer[27:], dtype=np.int16).reshape(256, 256).transpose()
).copy()
buffer = zip_file.read(file_names[2])
self._thresh = np.frombuffer(buffer[27:], dtype=np.int16).copy() >> 8
self._thresh = np.fliplr(
np.array([self._reverseBits(x) for x in self._thresh])
.reshape(256, 256)
.transpose()
)
@property
def filename(self):
return self.__filename
@property
def maskPixels(self):
"""Accessor for the mask pixels [0, 1]
Returns
----------
:obj:`numpy.ndarray` (256, 256)
The information which pixels are to be masked"""
return 1 - (self._mask // 256)
@maskPixels.setter
def maskPixels(self, mask_pixels):
self._mask = (1 - mask_pixels) * 256
@property
def testPixels(self):
"""Accessor for the test pixels
Returns
----------
:obj:`numpy.ndarray` (256, 256)"""
return self._test
@property
def thresholdPixels(self):
"""Accessor for the pixel thresholds [0, 15]
Returns
----------
:obj:`numpy.ndarray` (256, 256)
The threshold information for each pixel"""
return self._thresh
[docs]def main():
import matplotlib.pyplot as plt
spx = SophyConfig("E:/W0028_H06/settings/W0028_H06_50V.spx")
print(spx.dacCodes())
# plt.matshow(spx.maskPixels()[::-1,:])
# plt.show()
# plt.matshow(spx.thresholdPixels()[::-1,:])
# plt.show()
print(spx.maskPixels().max())
thresh = spx.thresholdPixels()
print("MAX", np.max(thresh))
print("MEAN", np.mean(thresh))
print("STDDEV", np.std(thresh))
plt.imshow(spx.maskPixels())
plt.show()
# plt.hist(thresh.flatten(),bins=16,range=[0,15])
# plt.show()
if __name__ == "__main__":
main()
# dac_setting = e.findall(".//entry[@class='sophy.medipix.SPMPXDACCollection']")
# dac_setting = dac_setting[0]
# dac_setting = dac_setting[0]
# In [68]: for element in dac_setting.findall(".//element[@class='java.util.Map.Entry']"):
# ...: key=element.find('key')
# ...:
# ...: entry=element.find('entry')
# ...: data = entry.find('data')
# ...: print(key.items()[-1][-1],data.items()[-1][-1])