def give_ave_series_data():
old_pkl = "/home/adnan/PycharmProjects/python3conversion/sphire/tests/pickle files/statistics/statistics.ave_series"
data_ave_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "data_ave_values.pkl"
data_ave_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "data_ave_head.pkl"
dill._dill._reverse_typemap["ObjectType"] = object
with io.open(
os.path.join(ABSOLUTE_PATH,
"pickle files/" + data_ave_values_name), "rb") as f1:
data_arras = pickle.load(f1, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + data_ave_head_name),
"rb") as f2:
data_heads = pickle.load(f2, encoding='latin1')
stack = []
for i in range(len(data_arras)):
stack.append(sp_utilities.numpy2em_python(data_arras[i]))
for key in data_heads[i]:
stack[i][key] = data_heads[i][key]
return stack
def give_ormq_data():
old_pkl = "/home/adnan/PycharmProjects/python3conversion/sphire/tests/pickle files/alignment.ormq"
image_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "ormq_image_values.pkl"
image_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "ormq_image_head.pkl"
crefim_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "ormq_crefim_values.pkl"
crefim_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "ormq_crefim_head.pkl"
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + image_values_name),
"rb") as f3:
image_data = pickle.load(f3, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + image_head_name),
"rb") as f4:
image_head = pickle.load(f4, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + crefim_values_name),
"rb") as f1:
crefim_data = pickle.load(f1, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + crefim_head_name),
"rb") as f2:
crefim_head = pickle.load(f2, encoding='latin1')
image = sp_utilities.numpy2em_python(image_data)
for keys in image_head:
image[keys] = image_head[keys]
crefim = sp_utilities.numpy2em_python(crefim_data)
for keys in crefim_head:
crefim[keys] = crefim_head[keys]
return image, crefim
def give_ali_vol_data():
old_pkl = "/home/adnan/PycharmProjects/python3conversion/sphire/tests/pickle files/applications.ali_vol"
vol_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "vol_values.pkl"
vol_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "vol_head.pkl"
refv_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "refv_values.pkl"
refv_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "refv_head.pkl"
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + vol_values_name),
"rb") as f3:
vol_data = pickle.load(f3, encoding='latin1')
with io.open(os.path.join(ABSOLUTE_PATH, "pickle files/" + vol_head_name),
"rb") as f4:
vol_head = pickle.load(f4, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + refv_values_name),
"rb") as f1:
refv_data = pickle.load(f1, encoding='latin1')
with io.open(os.path.join(ABSOLUTE_PATH, "pickle files/" + refv_head_name),
"rb") as f2:
refv_head = pickle.load(f2, encoding='latin1')
vol = sp_utilities.numpy2em_python(vol_data)
for keys in vol_head:
vol[keys] = vol_head[keys]
refv = sp_utilities.numpy2em_python(refv_data)
for keys in refv_head:
refv[keys] = refv_head[keys]
return vol, refv
def create_mask(size, index_particle_pixels, fraction_size=0.25):
mask = numpy.zeros(size)
rand_pixel_selection = numpy.random.choice(
range(len(index_particle_pixels[0])),
size=int(len(index_particle_pixels[0]) * fraction_size),
replace=False,
)
rand_pixel_selection = (
index_particle_pixels[0][rand_pixel_selection],
index_particle_pixels[1][rand_pixel_selection],
)
mask[rand_pixel_selection] = 1.0
return_mask = sp_utilities.numpy2em_python(mask)
return return_mask
def give_alignment_shc_data():
old_pkl = "/home/adnan/PycharmProjects/python3conversion/sphire/tests/pickle files/alignment.shc"
xfomimg_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "xfomimg_values.pkl"
xfomimg_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "xfomimg_head.pkl"
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + xfomimg_values_name),
"rb") as f3:
xfomimg_data = pickle.load(f3, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + xfomimg_head_name),
"rb") as f4:
xfomimg_head = pickle.load(f4, encoding='latin1')
xformimg = sp_utilities.numpy2em_python(xfomimg_data)
for keys in xfomimg_head:
xformimg[keys] = xfomimg_head[keys]
return xformimg
def give_projection_prgl_data():
old_pkl = "/home/adnan/PycharmProjects/python3conversion/sphire/tests/pickle files/projection.prgl"
volft_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "volft_values.pkl"
volft_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "volft_head.pkl"
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + volft_values_name),
"rb") as f3:
volft_data = pickle.load(f3, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + volft_head_name),
"rb") as f4:
volft_head = pickle.load(f4, encoding='latin1')
volft = sp_utilities.numpy2em_python(volft_data)
for keys in volft_head:
volft[keys] = volft_head[keys]
return volft
def give_ali2d_single_iter_data():
numr = [
1, 1, 8, 2, 9, 16, 3, 25, 32, 4, 57, 32, 5, 89, 32, 6, 121, 64, 7, 185,
64, 8, 249, 64, 9, 313, 64, 10, 377, 64, 11, 441, 128, 12, 569, 128,
13, 697, 128, 14, 825, 128, 15, 953, 128, 16, 1081, 128, 17, 1209, 128,
18, 1337, 128, 19, 1465, 128, 20, 1593, 128, 21, 1721, 256, 22, 1977,
256, 23, 2233, 256, 24, 2489, 256, 25, 2745, 256, 26, 3001, 256, 27,
3257, 256, 28, 3513, 256, 29, 3769, 256
]
wr = [
25.132741228718345, 12.566370614359172, 4.71238898038469,
6.283185307179586, 7.853981633974483, 2.356194490192345,
2.748893571891069, 3.141592653589793, 3.5342917352885173,
3.9269908169872414, 1.0799224746714913, 1.1780972450961724,
1.2762720155208536, 1.3744467859455345, 1.4726215563702154,
1.5707963267948966, 1.6689710972195777, 1.7671458676442586,
1.8653206380689396, 1.9634954084936207, 0.5154175447295755,
0.5399612373357456, 0.5645049299419159, 0.5890486225480862,
0.6135923151542565, 0.6381360077604268, 0.662679700366597,
0.6872233929727672, 0.7117670855789375
]
cs = [0.0, 0.0]
cnx = 36
cny = 36
xrng = 4
yrng = 4
step = 1
old_pkl = "/home/adnan/PycharmProjects/python3conversion/sphire/tests/pickle files/alignment.ali2d_single_iter"
data_values_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "_data_values.pkl"
data_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "_data_head.pkl"
tavg_value_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "_tavg_values.pkl"
tavg_head_name = os.path.splitext(
os.path.basename(old_pkl))[0] + "_tavg_head.pkl"
dill._dill._reverse_typemap["ObjectType"] = object
# print(data_values_name)
# print(os.path.join(ABSOLUTE_PATH, "pickle files/" + data_values_name))
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + data_values_name),
"rb") as f1:
data_arras = pickle.load(f1, encoding='latin1')
with io.open(os.path.join(ABSOLUTE_PATH, "pickle files/" + data_head_name),
"rb") as f2:
data_heads = pickle.load(f2, encoding='latin1')
with io.open(
os.path.join(ABSOLUTE_PATH, "pickle files/" + tavg_value_name),
"rb") as f3:
tavg_data = pickle.load(f3, encoding='latin1')
with io.open(os.path.join(ABSOLUTE_PATH, "pickle files/" + tavg_head_name),
"rb") as f4:
tavg_head = pickle.load(f4, encoding='latin1')
data = []
for i in range(len(data_arras)):
data.append(sp_utilities.numpy2em_python(data_arras[i]))
for key in data_heads[i]:
data[i][key] = data_heads[i][key]
tavg = sp_utilities.numpy2em_python(tavg_data)
for keys in tavg_head:
tavg[keys] = tavg_head[keys]
return data, numr, wr, cs, tavg, cnx, cny, xrng, yrng, step