Added hdf reader, but there still seems to be a memory leakage bug.
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jupfi
parent
57d9274199
commit
62c8863a4e
5 changed files with 187 additions and 2 deletions
2
extern/limedriver
vendored
2
extern/limedriver
vendored
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@ -1 +1 @@
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Subproject commit 3d1c7bdf2ce95fb69f5a89b195a0f6e18496f97f
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Subproject commit f9d86bd4dea17250d9b0267936fb99d35a4ad1fd
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@ -17,7 +17,10 @@ classifiers = [
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requires = [
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"setuptools",
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"wheel",
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"Cython"
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"Cython",
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"h5py",
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"numpy",
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'matplotlib',
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]
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build-backend = "setuptools.build_meta"
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@ -1 +1,2 @@
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import limedriver.binding
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import limedriver.hdf_reader
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149
src/limedriver/hdf_reader.py
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149
src/limedriver/hdf_reader.py
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@ -0,0 +1,149 @@
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import h5py
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import numpy as np
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import matplotlib.pyplot as plt
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# class for accessing data of stored HDF5 file this is from the limr program by andrin doll
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class HDF():
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def __init__(self, filename = ''):
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# check first for the filename provided
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if filename != '':
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self.HDFsrc = filename
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else:
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self.HDFsrc = ''
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# get data
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self.__get_data()
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# just an alias for __init__ that does load a specific file
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def load(self, filename = ''):
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self.__init__(filename)
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# gets the data of the file
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def __get_data(self):
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if (self.HDFsrc == '') | (self.HDFsrc == []):
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# initialize all as empty
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self.tdy = []
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self.tdx = []
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self.attrs = []
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self.parsoutp = {}
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self.parvar = {}
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else:
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f = h5py.File(self.HDFsrc, 'r')
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print("opened file")
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HDFkeys = list(f.keys())
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for ii, HDFkey in enumerate(HDFkeys):
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if ii == 0:
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# initialize data array
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dsize = f[HDFkey].shape
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inddim = dsize[0]
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self.tdy = np.zeros((int(dsize[1]/2), int(dsize[0] * len(HDFkeys))),dtype=np.complex_)
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print("initialize")
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# initialize the output objects
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self.attrs = [dynclass() for jj in range(len(HDFkeys))]
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print("get the attribute keys")
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# get the attribute keys
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self.parsoutp = {}
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ii_oupargs = 0
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for item in f[HDFkey].attrs.items():
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print(item)
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itemname = item[0][5:]
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itemarg = item[0][1:4]
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if not ('///' in itemarg):
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self.parsoutp[itemarg] = [ item[1], itemname]
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else:
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self.parsoutp['//'+str(ii_oupargs)] = [ item[1], itemname]
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ii_oupargs+=1
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print("end of loop")
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print("look for vars")
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# look for eventual parvar lists
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self.parvar = {}
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for item in f.attrs.items():
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self.parvar[item[0]] = item[1]
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# Get the data
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data_raw = np.array(f[HDFkey])
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try:
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self.tdy[:,ii*inddim:(ii+1)*inddim] = np.transpose(np.float_(data_raw[:,::2])) + 1j*np.transpose(np.float_(data_raw[:,1::2]))
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except:
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pass
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# Get the arguments
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ii_oupargs = 0
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for item in f[HDFkey].attrs.items():
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itemname = item[0][5:]
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itemarg = item[0][1:4]
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if not ('///' in itemarg):
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setattr(self.attrs[ii], itemarg, item[1])
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else:
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setattr(self.attrs[ii], '//'+str(ii_oupargs), item[1])
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ii_oupargs+=1
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f.close()
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srate_MHz = getattr(self.attrs[0], 'sra')*1e-6
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self.tdx = 1/srate_MHz*np.arange(self.tdy.shape[0])
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# get an argument by matching the text description
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def attr_by_txt(self, pattern):
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for key in sorted(self.parsoutp):
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if pattern in self.parsoutp[key][1]: # pattern match
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attr = getattr(self.attrs[0], key)
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try:
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ouparr = np.zeros( ( len(attr), len(self.attrs)), attr.dtype)
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except:
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ouparr = np.zeros( ( 1, len(self.attrs)), attr.dtype)
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for ii in np.arange(len(self.attrs)):
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ouparr[:,ii] = getattr(self.attrs[ii], key)
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return np.transpose(ouparr)
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print('Problem obtaining the attribute from the description using the pattern ' + pattern + '!')
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print('Valid descriptions are: ')
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self.print_params()
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# get an argument by key
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def attr_by_key(self, key):
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if key in dir(self.attrs[0]):
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attr = getattr(self.attrs[0], key)
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try:
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ouparr = np.zeros( ( len(attr), len(self.attrs)), attr.dtype)
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except:
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ouparr = np.zeros( ( 1, len(self.attrs)), attr.dtype)
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for ii in np.arange(len(self.attrs)):
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ouparr[:,ii] = getattr(self.attrs[ii], key)
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return np.transpose(ouparr)
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print('Problem obtaining the attribute from key ' + key + '!')
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print('Valid keys are: ')
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self.print_params()
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# print the arguments
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def print_params(self, ouponly = False):
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for key in sorted(self.parsoutp):
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val = getattr(self.attrs[0], key)
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if not('//' in key): # input argument?
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if ouponly: continue;
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print('{:<5}: {:>50} {:<25}'.format(key, val, self.parsoutp[key][1]))
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def plot_dta(self):
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plt.plot(self.tdx, self.tdy.real)
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plt.xlabel('$t$ [$\mu$s]')
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plt.ylabel('$y$ [Counts]')
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plt.show()
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# empty class to store dynamic attributes, basically for the attributes in HDF keys
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class dynclass:
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pass
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@ -8,6 +8,8 @@ from libc.string cimport memcpy, strcpy
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from libcpp.string cimport string
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import pathlib
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cdef extern from "limedriver.h":
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cdef struct LimeConfig_t:
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float srate
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@ -149,8 +151,33 @@ cdef class PyLimeConfig:
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def __dealloc__(self):
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if self._config is not NULL:
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free(self._config.p_frq)
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free(self._config.p_dur)
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free(self._config.p_dur_smp)
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free(self._config.p_offs)
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free(self._config.p_amp)
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free(self._config.p_frq_smp)
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free(self._config.p_pha)
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free(self._config.p_phacyc_N)
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free(self._config.p_phacyc_lev)
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free(self._config.am_frq)
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free(self._config.am_pha)
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free(self._config.am_depth)
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free(self._config.am_mode)
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free(self._config.am_frq_smp)
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free(self._config.fm_frq)
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free(self._config.fm_pha)
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free(self._config.fm_width)
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free(self._config.fm_mode)
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free(self._config.fm_frq_smp)
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free(self._config.p_c0_en)
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free(self._config.p_c1_en)
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free(self._config.p_c2_en)
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free(self._config.p_c3_en)
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free(self._config)
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@property
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def srate(self):
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return self._config.srate
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@ -802,3 +829,8 @@ cdef class PyLimeConfig:
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def run(self):
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return run_experiment_from_LimeCfg(self._config[0])
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def get_path(self):
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path = self.save_path + self.file_stamp + '_' + self.file_pattern + '.h5'
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path = pathlib.Path(path).absolute()
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return path
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