def get_petlink32_stats():
"""Get information about the current petlink32 listmode data. """
descriptor = [
{
'name': 'n_packets',
'type': 'long',
'value': None
},
{
'name': 'n_unknown',
'type': 'uint',
'value': None
},
{
'name': 'n_prompt',
'type': 'uint',
'value': None
},
{
'name': 'n_delayed',
'type': 'uint',
'value': None
},
{
'name': 'n_elapsedtime',
'type': 'uint',
'value': None
},
{
'name': 'n_deadtime',
'type': 'uint',
'value': None
},
{
'name': 'n_motion',
'type': 'uint',
'value': None
},
{
'name': 'n_gating',
'type': 'uint',
'value': None
},
{
'name': 'n_tracking',
'type': 'uint',
'value': None
},
{
'name': 'n_control',
'type': 'uint',
'value': None
},
]
r = call_c_function(petlink32_c.get_petlink32_stats, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'get_petlink32_stats' was unsuccesful.",
r.status, 'petlink32_c.get_petlink32_stats')
return r.dictionary
def get_info():
"""Extract information from Siemens binary physiological data file: get information from global memory structure. """
descriptor = [
{
'name': 'n_samples_breathing',
'type': 'uint',
'value': None
},
{
'name': 'n_samples_ecg_I',
'type': 'uint',
'value': None
},
{
'name': 'n_samples_ecg_aVF',
'type': 'uint',
'value': None
},
{
'name': 'n_samples_pulse_ox',
'type': 'uint',
'value': None
},
{
'name': 'n_samples_external',
'type': 'uint',
'value': None
},
]
r = call_c_function(physiological_c.get_info, descriptor)
if not r.status == status_success():
raise ErrorInCFunction("The execution of get_info was unsuccesful.",
r.status, 'get_info')
return r.dictionary
def uncompress_static_projection(offsets, counts, locations, N_u, N_v):
"""Get the static projection corresponding to a given time bin of the current dynamic projection data. """
N_counts = counts.size
N_axial = offsets.shape[0]
N_azimuthal = offsets.shape[1]
descriptor = [
{
'name': 'N_counts',
'type': 'uint',
'value': N_counts
},
{
'name': 'N_axial',
'type': 'uint',
'value': N_axial
},
{
'name': 'N_azimuthal',
'type': 'uint',
'value': N_azimuthal
},
{
'name': 'N_u',
'type': 'uint',
'value': N_u
},
{
'name': 'N_v',
'type': 'uint',
'value': N_v
},
{
'name': 'offsets',
'type': 'array',
'value': offsets
},
{
'name': 'counts',
'type': 'array',
'value': counts
},
{
'name': 'locations',
'type': 'array',
'value': locations
},
{
'name': 'projection',
'type': 'array',
'value': None,
'dtype': np.uint32,
'size': (N_axial, N_azimuthal, N_u, N_v)
},
]
r = call_c_function(petlink32_c.uncompress_static_projection, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'uncompress_static_projection' was unsuccesful.",
r.status, 'petlink32_c.uncompress_static_projection')
return r.dictionary
def status_parameter_error():
"""Returns the value returned by the function calls to the library in case of parameter error. """
r = call_c_function(petlink32_c.status_parameter_error, [{
'name': 'return_value',
'type': 'int',
'value': None
}])
return r.return_value
def status_success():
"""Returns the value returned by the function calls to the library in case of success. """
r = call_c_function(physiological_c.status_success, [{
'name': 'return_value',
'type': 'int',
'value': None
}])
return r.return_value
def status_decode_error():
"""Returns the value returned by the function calls to the library in case of error decoding a file. """
r = call_c_function(physiological_c.status_decode_error, [{
'name': 'return_value',
'type': 'int',
'value': None
}])
return r.return_value
def status_unhandled_error():
"""Returns the value returned by the function calls to the library in case of unhandled error. """
r = call_c_function(physiological_c.status_unhandled_error, [{
'name': 'return_value',
'type': 'int',
'value': None
}])
return r.return_value
def free_memory():
"""Free memory"""
r = call_c_function(petlink32_c.free_memory, [])
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'free_memory' was unsuccesful.", r.status,
'petlink32_c.free_memory')
return r.dictionary
def petlink32_info(filename, n_packets):
"""Extracts summary information from a listmode binary file. """
descriptor = [
{
'name': 'filename',
'type': 'string',
'value': filename,
'size': len(filename)
},
{
'name': 'n_packets',
'type': 'int',
'value': n_packets
},
{
'name': 'n_prompts',
'type': 'int',
'value': None
},
{
'name': 'n_delayed',
'type': 'int',
'value': None
},
{
'name': 'n_tags',
'type': 'int',
'value': None
},
{
'name': 'n_time',
'type': 'int',
'value': None
},
{
'name': 'n_motion',
'type': 'int',
'value': None
},
{
'name': 'n_monitoring',
'type': 'int',
'value': None
},
{
'name': 'n_control',
'type': 'int',
'value': None
},
]
r = call_c_function(petlink32_c.petlink32_info, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of petlink32_info was unsuccesful.", r.status,
'petlink32_c.petlink32_info')
return r.dictionary
def load_data(filename):
"""Extract information from Siemens binary physiological data file: load_interfile data to global memory structure """
descriptor = [
{
'name': 'filename',
'type': 'string',
'value': filename,
'size': len(filename)
},
]
r = call_c_function(physiological_c.load_data, descriptor)
if not r.status == status_success():
raise ErrorInCFunction("The execution of load_data was unsuccesful.",
r.status, 'load_data')
return r.dictionary
def test_library():
"""Test whether the C library responds. Used in the package testing. """
number = 134 # a (lucky) number
descriptor = [
{
'name': 'input',
'type': 'int',
'value': number
},
{
'name': 'output',
'type': 'int',
'value': None
},
]
r = call_c_function(physiological_c.echo, descriptor)
return r.output == number
def test_library_petlink32_c():
"""Test whether the C library petlink32_c responds. """
number = 101 # just a number
descriptor = [
{
'name': 'input',
'type': 'int',
'value': number
},
{
'name': 'output',
'type': 'int',
'value': None
},
]
r = call_c_function(petlink32_c.echo, descriptor)
return r.output == number
def get_dynamic_projection_info():
"""Get information about the current dynamic projection data. """
descriptor = [
{
'name': 'N_time_bins',
'type': 'uint',
'value': None
},
{
'name': 'N_counts',
'type': 'long',
'value': None
},
]
r = call_c_function(petlink32_c.get_dynamic_projection_info, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'get_dynamic_projection_info' was unsuccesful.",
r.status, 'petlink32_c.get_dynamic_projection_info')
return r.dictionary
def petlink32_bin_addresses(filename, n_packets):
"""Extract list of bin indexes from listmode data. """
descriptor = [
{
'name': 'filename',
'type': 'string',
'value': filename,
'size': len(filename)
},
{
'name': 'n_packets',
'type': 'int',
'value': n_packets
},
{
'name': 'bin_addresses',
'type': 'array',
'value': None,
'dtype': np.int32,
'size': (1, n_packets)
},
{
'name': 'n_prompts',
'type': 'int',
'value': None
},
{
'name': 'n_delayed',
'type': 'int',
'value': None
},
{
'name': 'n_tags',
'type': 'int',
'value': None
},
{
'name': 'n_time',
'type': 'int',
'value': None
},
{
'name': 'n_motion',
'type': 'int',
'value': None
},
{
'name': 'n_monitoring',
'type': 'int',
'value': None
},
{
'name': 'n_control',
'type': 'int',
'value': None
},
]
r = call_c_function(petlink32_c.petlink32_bin_addresses, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of petlink32_bin_addresses was unsuccesful.",
r.status, 'petlink32_c.petlink32_bin_addresses')
return r.dictionary
def petlink32_to_static_sinogram(filename, n_packets, n_radial_bins, n_angles,
n_sinograms):
"""Make static sinogram from listmode data. """
descriptor = [
{
'name': 'filename',
'type': 'string',
'value': filename,
'size': len(filename)
},
{
'name': 'n_packets',
'type': 'long',
'value': n_packets
},
{
'name': 'n_radial_bins',
'type': 'int',
'value': n_radial_bins
},
{
'name': 'n_angles',
'type': 'int',
'value': n_angles
},
{
'name': 'n_sinograms',
'type': 'int',
'value': n_sinograms
},
{
'name': 'sinogram',
'type': 'array',
'value': None,
'dtype': np.int32,
'size': (n_radial_bins, n_angles, n_sinograms)
},
{
'name': 'packets_unknown',
'type': 'int',
'value': None
},
{
'name': 'packets_prompt',
'type': 'int',
'value': None
},
{
'name': 'packets_delayed',
'type': 'int',
'value': None
},
{
'name': 'packets_elapsedtime',
'type': 'int',
'value': None
},
{
'name': 'packets_deadtime',
'type': 'int',
'value': None
},
{
'name': 'packets_motion',
'type': 'int',
'value': None
},
{
'name': 'packets_gating',
'type': 'int',
'value': None
},
{
'name': 'packets_tracking',
'type': 'int',
'value': None
},
{
'name': 'packets_control',
'type': 'int',
'value': None
},
]
r = call_c_function(petlink32_c.petlink32_to_static_sinogram, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'petlink32_to_static_sinogram' was unsuccesful.",
r.status, 'petlink32_c.petlink32_to_static_sinogram')
return r.dictionary
def petlink32_to_dynamic_projection(filename, n_packets, n_radial_bins,
n_angles, n_sinograms, time_bins, n_axial,
n_azimuthal, angular_step_axial,
angular_step_azimuthal, size_u, size_v,
n_u, n_v):
"""Make dynamic compressed projection from list-mode data. """
descriptor = [
{
'name': 'filename',
'type': 'string',
'value': filename,
'size': len(filename)
},
{
'name': 'n_packets',
'type': 'long',
'value': n_packets
},
{
'name': 'n_radial_bins',
'type': 'uint',
'value': n_radial_bins
},
{
'name': 'n_angles',
'type': 'uint',
'value': n_angles
},
{
'name': 'n_sinograms',
'type': 'uint',
'value': n_sinograms
},
{
'name': 'n_time_bins',
'type': 'uint',
'value': len(time_bins)
},
{
'name': 'time_bins',
'type': 'array',
'value': np.int32(time_bins)
},
{
'name': 'n_axial',
'type': 'uint',
'value': n_axial
},
{
'name': 'n_azimuthal',
'type': 'uint',
'value': n_azimuthal
},
{
'name': 'angular_step_axial',
'type': 'float',
'value': angular_step_axial
},
{
'name': 'angular_step_azimuthal',
'type': 'float',
'value': angular_step_azimuthal
},
{
'name': 'size_u',
'type': 'float',
'value': size_u
},
{
'name': 'size_v',
'type': 'float',
'value': size_v
},
{
'name': 'n_u',
'type': 'uint',
'value': n_u
},
{
'name': 'n_v',
'type': 'uint',
'value': n_v
},
]
r = call_c_function(petlink32_c.petlink32_to_dynamic_projection,
descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'petlink32_to_dynamic_compressed_sinogram' was unsuccesful.",
r.status, 'petlink32_c.petlink32_to_dynamic_compressed_sinogram')
return r.dictionary
def get_data(n_samples_breathing, n_samples_ecg_I, n_samples_ecg_aVF,
n_samples_pulse_ox, n_samples_external):
"""Extract information from Siemens binary physiological data file: get data from global memory strucutre. """
descriptor = [
{
'name': 'n_samples_breathing',
'type': 'uint',
'value': n_samples_breathing
},
{
'name': 'n_samples_ecg_I',
'type': 'uint',
'value': n_samples_ecg_I
},
{
'name': 'n_samples_ecg_aVF',
'type': 'uint',
'value': n_samples_ecg_aVF
},
{
'name': 'n_samples_pulse_ox',
'type': 'uint',
'value': n_samples_pulse_ox
},
{
'name': 'n_samples_external',
'type': 'uint',
'value': n_samples_external
},
{
'name': 'samples_breathing',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_breathing)
},
{
'name': 'samples_ecg_I',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_ecg_I)
},
{
'name': 'samples_ecg_aVF',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_ecg_aVF)
},
{
'name': 'samples_pulse_ox',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_pulse_ox)
},
{
'name': 'samples_external',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_external)
},
{
'name': 'triggers_breathing',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_breathing)
},
{
'name': 'triggers_ecg_I',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_ecg_I)
},
{
'name': 'triggers_ecg_aVF',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_ecg_aVF)
},
{
'name': 'triggers_pulse_ox',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_pulse_ox)
},
{
'name': 'triggers_external',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (n_samples_external)
},
]
r = call_c_function(physiological_c.get_data, descriptor)
if not r.status == status_success():
raise ErrorInCFunction("The execution of get_data was unsuccesful.",
r.status, 'get_data')
return r.dictionary
def get_static_projection_info(time_bin):
"""Get information about a time bin of the current dynamic projection data. """
descriptor = [
{
'name': 'time_bin',
'type': 'uint',
'value': time_bin
},
{
'name': 'time_start',
'type': 'uint',
'value': None
},
{
'name': 'time_end',
'type': 'uint',
'value': None
},
{
'name': 'N_counts',
'type': 'uint',
'value': None
},
{
'name': 'N_axial',
'type': 'uint',
'value': None
},
{
'name': 'N_azimuthal',
'type': 'uint',
'value': None
},
{
'name': 'angular_step_axial',
'type': 'float',
'value': None
},
{
'name': 'angular_step_azimuthal',
'type': 'float',
'value': None
},
{
'name': 'size_u',
'type': 'float',
'value': None
},
{
'name': 'size_v',
'type': 'float',
'value': None
},
{
'name': 'N_u',
'type': 'uint',
'value': None
},
{
'name': 'N_v',
'type': 'uint',
'value': None
},
]
r = call_c_function(petlink32_c.get_static_projection_info, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'get_static_projection_info' was unsuccesful.",
r.status, 'petlink32_c.get_static_projection_info')
return r.dictionary
def get_static_projection(time_bin):
"""Get the static projection corresponding to a given time bin of the current dynamic projection data. """
info = get_static_projection_info(time_bin)
N_counts = info['N_counts']
N_axial = info['N_axial']
N_azimuthal = info['N_azimuthal']
descriptor = [
{
'name': 'time_bin',
'type': 'uint',
'value': time_bin
},
{
'name': 'time_start',
'type': 'uint',
'value': None
},
{
'name': 'time_end',
'type': 'uint',
'value': None
},
{
'name': 'N_counts',
'type': 'uint',
'value': None
},
{
'name': 'N_axial',
'type': 'uint',
'value': None
},
{
'name': 'N_azimuthal',
'type': 'uint',
'value': None
},
{
'name': 'angular_step_axial',
'type': 'float',
'value': None
},
{
'name': 'angular_step_azimuthal',
'type': 'float',
'value': None
},
{
'name': 'size_u',
'type': 'float',
'value': None
},
{
'name': 'size_v',
'type': 'float',
'value': None
},
{
'name': 'N_u',
'type': 'uint',
'value': None
},
{
'name': 'N_v',
'type': 'uint',
'value': None
},
{
'name': 'offsets',
'type': 'array',
'value': None,
'dtype': np.uint32,
'size': (N_axial, N_azimuthal)
},
{
'name': 'counts',
'type': 'array',
'value': None,
'dtype': np.float32,
'size': N_counts
},
{
'name': 'locations',
'type': 'array',
'value': None,
'dtype': np.uint16,
'size': (N_counts, 3)
},
]
r = call_c_function(petlink32_c.get_static_projection, descriptor)
if not r.status == status_success():
raise ErrorInCFunction(
"The execution of 'get_static_projection' was unsuccesful.",
r.status, 'petlink32_c.get_static_projection')
return r.dictionary
