def test_read(self):
logging.info('Checking reading example data')
data = cbf.read('../examples/in16c_010001.cbf')
# Random points of the image
self.assertEqual(data.data[0][0], 1)
self.assertEqual(data.data[0][-1], -2) # Point with extreme value
self.assertEqual(data.data[0][-2], 1)
self.assertEqual(data.data[-1][0], -2) # Point with extreme value
self.assertEqual(data.data[-1][-1], -2) # Point with extreme value
self.assertEqual(data.data[-1][-2], 0)
self.assertEqual(data.data[334][262], 1680)
self.assertEqual(data.data[125][127], -2) # Point with extreme value
self.assertEqual(data.data[357][271], 214)
data = cbf.read('../examples/run2_1_00148.cbf')
# Random points of the image
self.assertEqual(data.data[1169][1006], 20)
self.assertEqual(data.data[1178][1030], 0)
self.assertEqual(data.data[1223][1015], 2068)
self.assertEqual(data.data[754][1859], 14)
self.assertEqual(data.data[777][1707], 16)
self.assertEqual(data.data[1302][1323], 98)
def show_image(self, im=None, lab='q', stack=1, **kwargs):
rc('text', usetex=False)
if not im: im = self.im
file = "%s_%s.cbf" % (self.basename, str(im).zfill(self.pad)
) #;print(filename)
# with open(file,'wb') as f:print(file)
content = cbf.read(file)
image = content.data
if stack > 1:
for i in range(1, stack):
filename = "%s_%s.cbf" % (self.basename, str(im + i).zfill(
self.pad)) #;print(filename)
image += cbf.read(filename).data
if 'caxis' in list(kwargs.keys()):
kwargs['caxis'] = list(np.array(kwargs['caxis']) *
stack) #; print(kwargs['caxis'])
if 'q' in lab:
labs = ['$q_x(A^{-1})$', '$q_y(A^{-1})$']
X, Y = self.qx, -self.qy
elif 'p' in lab:
labs = ['', ''] #['$p_x$','$p_y$']
X, Y = self.pX, self.pY
elif 'x' in lab:
labs = ['$x(mm)$', '$y(mm)$']
px, py = self.pxy
X, Y = self.pX * px * 1e3, self.pY * py * 1e3
return dsp.stddisp(im=[X, Y, image],
labs=labs,
pOpt='ptX',
title="%s" % os.path.basename(file),
**kwargs)
def headercbf(filename):
if isfile(filename):
f = cbf.read(filename)
return f.metadata
else:
print("file ", filename, " does not exist!")
return 0
def loadcbf(filename):
if isfile(filename):
f = cbf.read(filename)
return f.data
else:
print("file ", filename, " does not exist!")
return 0
def loadCBFContent(self):
# -----
valid = (self.full_image_path is not None)
# -----
newPath = self.image_path % self.image_tracking_widget_layout.image_num_spinbox.value(
)
if ((self.full_image_path != newPath)
or (self.canvas.fullImagePath != newPath)):
self.full_image_path = newPath
try:
self.cbfContent = cbf.read(self.full_image_path,
metadata=False)
self.numpyArrayWithData = self.cbfContent.data
# -----
valid = True
except:
# Inform user that an error occurred
logging.getLogger('user_level_log').error(
'Error loading CBF image: \'%s\'!' %
str(self.full_image_path))
# Clean showed image
self.loadBlanckImage()
# return invalid
valid = False
return valid
def getHeader(self, fileName):
"""
Header is python dict {}
"""
content = cbf.read(fileName, metadata=True, parse_miniheader=True)
header = content.miniheader
return header
def getData(self, fileName):
"""
Data is float numpy array
"""
content = cbf.read(fileName)
data = np.array(content.data).astype(float)
return data
def getDataHeader(self, fileName):
"""
Data is float numpy array
Header is python dict {}
"""
content = cbf.read(fileName, metadata=True, parse_miniheader=True)
data = np.array(content.data).astype(float)
header = content.miniheader
return (data, header)
def load_cbf(self, fig):
try:
content = cbf.read(fig)
except: #UnicodeDecodeError
self.i = self.i + self.mode
print(colors.red + 'error reading file' + colors.black)
self.import_exp()
return
numpy_array_with_data = content.data
header_metadata = content.metadata
# print(colors.blue,header_metadata,colors.black)
return numpy_array_with_data
def __init__(self, file, sym=1, pad=None):
basename = file.split('_')
self.im = int(basename[-1].replace('.cbf', ''))
self.basename = '_'.join(basename[:-1])
file_ids = [
int(f.split('_')[-1].replace('.cbf', ''))
for f in glob.glob(self.basename + '*.cbf')
]
if pad:
self.pad = pad
else:
self.pad = int(np.log10(max(file_ids))) + 1 #;print(self.pad)
ls = np.array(
check_output("head -n25 %s" % file,
shell=True).decode().split('\n'))
px_str = ls[['Pixel_size' in l for l in ls]][0]
D_str = ls[['Detector_distance' in l for l in ls]][0] #;print(D_str)
lam_str = ls[["Wavelength" in l for l in ls]][0]
self.pxy = np.array(re.findall("\d+e-\d+", px_str), dtype=float)
self.D = 1 #float(re.findall("\d+.\d+",D_str)[0])
self.lam = float(re.findall("\d+.\d+", lam_str)[0])
shape = np.array(cbf.read(file).data.shape)
self.image = cbf.read(file).data
if sym:
Nx, Ny = np.array(shape / 2, dtype=int)
self.Nx, self.Ny = Nx, Ny
self.pX, self.pY = np.meshgrid(np.arange(-Nx, Nx + 1),
np.arange(-Ny, Ny + 1))
else:
Nx, Ny = shape
# self.pX,self.pY = np.meshgrid(np.arange(Nx),np.arange(Ny))
self.pX, self.pY = np.meshgrid(np.arange(Nx),
np.flipud(np.arange(Ny)))
self.qx, self.qy = self.px2s(self.pX, self.pY)
def test_write(self):
for i in range(1000):
logging.info('start')
test_file = 'test.cbf'
# Ensure that file does not exist
try:
os.remove(test_file)
except OSError:
pass
# 65536
# 66600 cannot compress at all
min_number = 0
max_number = 66600
max_number = 600
max_number = 2147483647 # max value int32
# max_number = 2147483648 # max value + 1int32 # will fail
numpy_array = numpy.random.randint(min_number, max_number,
(500, 400)).astype('int32')
numpy_array[0][0] = max_number
# numpy_array[0][0] = -1
# numpy_array = numpy.empty((500, 400)).astype('int32')
# numpy_array.fill(max_number)
print(numpy_array[0][0])
cbf.write(test_file, numpy_array)
content = cbf.read(test_file)
if not (numpy_array == content.data).all():
print('NOT SAME')
print((numpy_array == content.data).sum())
print(content.data)
print(content.metadata)
print(content.metadata)
print(i)
self.assertTrue((numpy_array == content.data).all())
# Remove test file
os.remove(test_file)
def test_write(self):
for i in range(1000):
logging.info('start')
test_file = 'test.cbf'
# Ensure that file does not exist
try:
os.remove(test_file)
except OSError:
pass
# 65536
# 66600 cannot compress at all
min_number = 0
max_number = 66600
max_number = 600
max_number = 2147483647 # max value int32
# max_number = 2147483648 # max value + 1int32 # will fail
numpy_array = numpy.random.randint(min_number, max_number, (500, 400)).astype('int32')
numpy_array[0][0] = max_number
# numpy_array = numpy.empty((500, 400)).astype('int32')
# numpy_array.fill(max_number)
print(numpy_array[0][0])
cbf.write(test_file, numpy_array)
content = cbf.read(test_file)
if not (numpy_array == content.data).all():
print('SAME')
print((numpy_array == content.data).sum())
print(content.data)
print(content.metadata)
print(content.metadata)
print(i)
self.assertTrue((numpy_array == content.data).all())
## There already exist packages for parsing these types of files
## But.. we can easily modify/update them if necessary!
import cbf
import os
from matplotlib import pyplot as plt
directory_in_str = str(input('Input directory file path: '))
#directory = os.fsencode(directory_in_str)
directory = directory_in_str
for file in os.listdir(directory):
filename = os.fsdecode(file)
if filename.endswith(".cbf"):
print('--> Reading in file: ',os.path.join(directory, filename))
cbf_file = os.path.join(directory, filename)
content = cbf.read(str(cbf_file))
numpy_array_with_data = content.data
header_metadata = content.metadata
# Plot image with matplot lib
plt.imshow(numpy_array_with_data, cmap='gray', vmax=1)
plt.show()
continue
else:
continue
def get_image(self, path):
if path.endswith(".cbf"):
return cbf.read(path).data
else:
return super().get_image(path)