def main():
for name in ("sp", "line", "depth", "mapping"):
filename = curdir / "spectra_files" / "{0}.wdf".format(name)
print("Testing: ", filename.as_posix())
# if debug=True, debug information will show in stderr
reader = WDFReader(filename, debug=True)
# Explicitly print into stdout
reader.print_info()
return
def read(filename):
loadables = pd.read_csv("config/import_config.csv")
extension = filename.split('.', 1)[1]
if (extension == "jpg"):
im = Image.open(filename)
im.save("temp.png")
data = hs.load("temp.png")
os.remove("temp.png")
return data
'''
if (extension == "txt"):
raw = np.genfromtxt(filename, delimiter="\t", skip_header=1, dtype=float, names =("X","Y","Wavelength","Intensity"))
#raw["X"] *= -1
xCoords = np.unique(raw["X"]).__len__()
yCoords = np.unique(raw["Y"]).__len__()
wavesize = int(np.shape(raw)[0]/xCoords/yCoords)
raw = np.sort(raw, axis=-1, order = ("Y","X","Wavelength"))
raw = (raw["Intensity"].reshape((xCoords, yCoords, wavesize)))
data = hs.signals.Signal1D(raw)
data.metadata.General.title = filename.split('.',1)[0]
data.axes_manager[0].name = 'x'
data.axes_manager[1].name = 'y'
data.axes_manager[2].name = 'wavelength'
data.axes_manager[0].units = "um"
data.axes_manager[1].units = "um"
data.axes_manager[2].units = "1/cm"
return data
'''
if (extension in loadables["extension"]):
if (loadables["extension" == extension]["signal"] == ""):
return hs.load(filename, signal_type=loadables["extension" == extension]["signal"])
else:
return hs.load(filename)
if (extension == "wdf"):
reader = WDFReader(filename)
reader.spectra = np.flip(reader.spectra,axis=2)
data = hs.signals.Signal1D(reader.spectra)
data.metadata.General.title = reader.title
data.metadata.General.authors = reader.username
data.axes_manager[0].name = 'x'
data.axes_manager[1].name = 'y'
data.axes_manager[2].name = 'wavelength'
data.axes_manager[0].units = str(reader.xpos_unit).replace('μ', 'u')
data.axes_manager[1].units = str(reader.ypos_unit).replace('μ', 'u')
data.axes_manager[2].units = str(reader.xlist_unit)
return data
else:
print("INVALID FILE TYPE")
def main():
filename = curdir / "spectra_files" / "sp.wdf"
reader = WDFReader(filename)
print("Measurement type is ", reader.measurement_type)
print("{0} Spectra obtained with {1} accumulations each".format(
reader.count, reader.accumulation_count))
# For ex1.wdf there is only 1 spectrum
assert reader.count == 1
wn = reader.xdata # wavenumber
sp = reader.spectra # spectrum / spectra in ccd counts
# For single spectrum the spectra has shape (point_per_spectrum, )
print(wn.shape, sp.shape)
if plot:
print("Use matplotlib to plot spectrum")
plt.figure(figsize=(6, 4))
plt.plot(wn, sp, label="Spectrum 1")
plt.xlabel("Wavenumber (1/cm)")
plt.ylabel("Intensity (ccd counts)")
plt.title("Spectrum from sp.wdf")
plt.show(block=False)
plt.tight_layout()
plt.pause(3)
plt.savefig(imgdir / "sp_spectra.png", dpi=100)
plt.close()
else:
print("No matplotlib, simply print the values")
print("Wavenumbers (1/cm): ", wn)
print("Intensities (ccd counts): ", sp)
return
def main():
filename = curdir / "spectra_files" / "line.wdf"
reader = WDFReader(filename)
assert reader.measurement_type == 3
# For mapping, xdata is still wavenumber
wn = reader.xdata
spectra = reader.spectra
assert wn.shape[0] == spectra.shape[1]
# Now spectra.shape becomes (i, j, spectrum)
print(wn.shape, spectra.shape)
if plot is True:
# Level the spectra with baseline intensity
spectra = spectra - spectra.min(axis=1, keepdims=True)
# Need to revert matrix for plotting
spectra = spectra.T
plt.figure(figsize=(6, 4))
# plot the first 5 spectra
for i in range(5):
plt.plot(wn, spectra[:, i], label="{0:d}".format(i))
plt.legend()
plt.xlabel("Wavenumber (1/cm)")
plt.ylabel("Intensity (ccd counts)")
plt.title("Spectra from line.wdf")
plt.show(block=False)
plt.pause(3)
plt.tight_layout()
plt.savefig(imgdir / "linscan.png", dpi=100)
plt.close()
else:
print("Wavenumber is like:", wn)
print("Spectra matrix is like: \n", spectra)
return
def exportFullImageSVG(path):
f3 = WDFReader(path)
img3 = mpimg.imread(f3.img, format="jpg")
img_x0, img_y0 = f3.img_origins
img_w, img_h = f3.img_dimensions
map_x = f3.xpos
map_y = f3.ypos
map_w = f3.map_info["x_span"]
map_h = f3.map_info["y_span"]
fig = plt.figure()
plt.imshow(img3, extent=(img_x0, img_x0 + img_w,
img_y0 + img_h, img_y0))
r = plt.Rectangle(xy=(map_x.min(), map_y.min()),
width=map_w,
height=map_h,
fill=False,
color='yellow')
plt.gca().add_patch(r)
plt.savefig(Path(path).expanduser().resolve().with_suffix('.fullmap.svg'))
fig.clear()
plt.close(fig)
def read_spectra(self):
# renishawWiRE is imported here so that its API changes would not block spectroscopy
from renishawWiRE import WDFReader # pylint: disable=import-outside-toplevel
wdf_file = WDFReader(self.filename)
try:
if wdf_file.measurement_type == 1: # single point spectra
table = self.single_reader(wdf_file)
elif wdf_file.measurement_type == 2: # series scan
table = self.series_reader(wdf_file)
elif wdf_file.measurement_type == 3: # line scan
table = self.map_reader(wdf_file)
finally:
wdf_file.close()
return table
def main():
filename = curdir / "spectra_files" / "mapping.wdf"
reader = WDFReader(filename)
assert reader.measurement_type == 3
wn = reader.xdata
spectra = reader.spectra
print(wn.shape, spectra.shape)
map_x = reader.xpos
map_y = reader.ypos
map_w = reader.map_info["x_span"]
map_h = reader.map_info["y_span"]
# w and h are the measure in xy coordinates
# Level the spectra
spectra = spectra - np.min(spectra, axis=2, keepdims=True)
peaks_a = peak_in_range(spectra, wn, [1295, 1340])
peaks_b = peak_in_range(spectra, wn, [1350, 1400])
ratio = peaks_a / peaks_b
extent = [0, map_w, map_h, 0]
if plot is True:
# Must provide the format to read the optical image
# img = mpimg.imread(reader.img, format="jpg")
img = PIL.Image.open(reader.img)
print(reader.img_cropbox)
# Desaturate the whitelight image
img1 = img.crop(box=reader.img_cropbox).convert("L")
plt.figure(figsize=(6, 6))
# Left, plot the white light image and rectangle area
# Show the image with upper origin extent See
# https://matplotlib.org/3.1.1/gallery/text_labels_and_annotations/text_alignment.html
plt.imshow(img1, alpha=0.5, cmap="hot", extent=extent)
# Right plot histogram of Peak A/B mapping
cm = plt.imshow(ratio,
interpolation="bicubic",
alpha=0.5,
cmap="viridis_r",
extent=extent,
vmin=0.5,
vmax=1.5)
plt.xlabel("Mapping x [μm]")
plt.ylabel("Mapping y [μm]")
cb = plt.colorbar(cm)
cb.ax.set_title("Ratio")
plt.title("50% Optical + 50% Raman")
plt.tight_layout()
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "map-overlay.png", dpi=100)
plt.close()
else:
pass
return
def main():
filename = curdir / "spectra_files" / "depth.wdf"
reader = WDFReader(filename)
# A depth scan
assert reader.measurement_type == 2
# For depth scan, xdata is still wavenumber
wn = reader.xdata
spectra = reader.spectra
x = reader.xpos
y = reader.ypos
z = reader.zpos
# print(x, y, z)
# In this example only z is non-zero
assert all([np.all(x == 0), np.all(y == 0), ~np.all(z == 0)])
assert reader.count == z.shape[0]
print(spectra, spectra.shape)
print(reader.count)
# Distance
wn = reader.xdata
spectra = reader.spectra
# Filter blank spectra
cond = np.where(spectra.mean(axis=1) > 0)[0]
z = z[cond]
spectra = spectra[cond, :]
# Data processing
spectra = spectra - spectra.min(axis=1, keepdims=True)
# Simply get accumulated counts between 1560 and 1620 cm^-1
peak_1 = peak_in_range(spectra, wn, range=[1560, 1620])
peak_2 = peak_in_range(spectra, wn, range=[2650, 2750])
ratio = peak_2 / peak_1
if plot is True:
# Level the spectra with baseline intensity
plt.figure(figsize=(6, 4))
plt.plot(z, peak_1 / peak_1.max(), "-o", label="G Peak")
# plt.plot(z, peak_2 / peak_2.max(), label="2D")
# plt.plot(z, ratio, label="2D/G")
plt.xlabel("Z [{0}]".format(str(reader.zpos_unit)))
plt.legend(loc=0)
plt.ylabel("Normed Intensity")
plt.title("Results from depth.wdf")
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "depth.png", dpi=100)
plt.close()
else:
print("Wavenumber is like:", wn)
print("Z-Distance is like:", z)
print("2D/G ratio is like: \n", ratio)
return
def main():
filename = curdir / "spectra_files" / "mapping.wdf"
reader = WDFReader(filename)
assert reader.measurement_type == 3
wn = reader.xdata
spectra = reader.spectra
print(wn.shape, spectra.shape)
x = reader.xpos
y = reader.ypos
w, h = reader.map_shape
print("The size of mapping is {0:d} * {1:d}".format(w, h))
# w and h are the measure in xy coordinates
# Level the spectra
spectra = spectra - np.min(spectra, axis=2, keepdims=True)
peaks_a = peak_in_range(spectra, wn, [1295, 1340])
peaks_b = peak_in_range(spectra, wn, [1350, 1400])
ratio = peaks_a / peaks_b
ratio_fl = ratio.flatten()
if plot is True:
plt.figure(figsize=(10, 5))
# Left plot histogram of Peak A/B ratio
plt.subplot(121)
plt.hist(ratio_fl, bins=50, range=(0.1, 2))
plt.xlabel("Ratio peak A / peak B")
plt.ylabel("Counts")
# Right plot histogram of Peak A/B mapping
plt.subplot(122)
plt.imshow(ratio,
interpolation="bicubic",
extent=[0, x.max() - x.min(),
y.max() - y.min(), 0],
vmin=0.5,
vmax=1.5)
plt.xlabel("Mapping x [μm]")
plt.ylabel("Mapping y [μm]")
cb = plt.colorbar()
cb.ax.set_title("Ratio")
plt.tight_layout()
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "mapping.png", dpi=100)
plt.close()
else:
pass
return
def exportCroppedImageSVG(path):
f3 = WDFReader(path)
img3_p = PIL.Image.open(f3.img)
img3_ = img3_p.crop(box=f3.img_cropbox)
map_w = f3.map_info["x_span"]
map_h = f3.map_info["y_span"]
extent = [0, map_w, map_h, 0]
fig = plt.figure()
plt.imshow(img3_, extent=extent)
plt.savefig(Path(path).expanduser().resolve().with_suffix('.cropped.svg'))
fig.clear()
plt.close(fig)
def call_exe(name, extras="", output=None):
filename = curdir / "spectra_files" / "{0}.wdf".format(name)
root = filename.parent
# clean up all
reader = WDFReader(filename)
assert reader is not None
for ext in (".csv", ".txt"):
for f in root.glob("*" + ext):
print(f)
os.remove(f)
# Initial name
cmd = "wdf-export {0} {1}".format(filename.as_posix(), extras)
if output is not None:
cmd += "-o {0}".format(output)
run = subprocess.run(cmd, shell=True)
assert run.returncode == 0
# Manually set output
if output is not None:
output = Path(output)
else:
if ".txt" not in extras:
output = filename.with_suffix(".csv")
else:
output = filename.with_suffix(".txt")
assert output.is_file() is True
# Read the data
if output.suffix == ".csv":
delimiter = ","
else:
delimiter = " "
data = np.genfromtxt(output, delimiter=delimiter, skip_header=1)
wn_data = data[:, 0]
spectra_data = data[:, 1:]
assert reader.xdata.shape[0] == wn_data.shape[0]
assert reader.count == spectra_data.shape[1]
spectra_reader = reader.spectra.reshape(reader.count,
reader.xdata.shape[0]).T
# Only do this for decreasing sequence
if reader.xdata[0] > reader.xdata[1]:
spectra_reader = spectra_reader[::-1, :]
print(spectra_reader)
print(spectra_data)
assert np.all(np.isclose(spectra_reader, spectra_data, 1e-3))
def main():
filename = curdir / "spectra_files" / "line.wdf"
reader = WDFReader(filename)
assert reader.measurement_type == 3
# For mapping, xdata is still wavenumber
wn = reader.xdata
spectra = reader.spectra
x = reader.xpos
y = reader.ypos
print(x.shape, y.shape)
assert x.shape[0] == y.shape[0] == spectra.shape[0]
# Distance
d = np.sqrt(x**2 + y**2)
wn = reader.xdata
spectra = reader.spectra
spectra = spectra - spectra.min(axis=1, keepdims=True)
# Simply get accumulated counts between 1560 and 1620 cm^-1
pos = np.where((wn >= 1560) & (wn <= 1620))[0]
cut = spectra[:, pos]
sum_cnt = np.sum(cut, axis=1)
if plot is True:
# Level the spectra with baseline intensity
plt.figure()
plt.plot(d - d[0], sum_cnt, "-o")
plt.xlabel("Distance (μm)")
plt.ylabel("Sum. Intensity (ccd counts)")
plt.title("Results from line.wdf")
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "linxy.png", dpi=100)
plt.close()
else:
print("Wavenumber is like:", wn)
print("Distance is like:", d)
print("Spectra matrix is like: \n", spectra)
return
def load_renishaw(fid, method='gaussian', threshold=0, longpass_cutoff=0):
'''
processes a PL map from the renishaw microraman tool
fid: path to .wdf file
threshold: minimum counts below which map pixels are considered background, set to nan
method: how to fit peak counts + wavelength ['gaussian', 'max']
longpass_cutoff: wavelength below which laser longpass is blocking counts. prevents gaussian fitting from
considering wavelengths blocked by filter.
'''
if method not in fitmethods_key:
raise ValueError(
f'Invalid fitting method - must be one of {list(fitmethods_key.items())}'
)
fitmethod = fitmethods_key[method]
d = WDFReader(fid)
d.img = np.asarray(Image.open(d.img))
if d.xlist_unit.name == 'Nanometre':
d.wl = d.xdata
d.shift = nmtoshift(d.wl, d.laser_length)
else:
d.wl = shifttonm(d.xdata, d.laser_length)
d.shift = d.xdata
longpass_mask = d.wl <= longpass_cutoff
d.maxcts = np.zeros(d.spectra.shape[:-1])
d.fwhm = np.zeros(d.spectra.shape[:-1])
d.peakwl = np.zeros(d.spectra.shape[:-1])
for m, n in tqdm(np.ndindex(d.maxcts.shape),
total=np.product(d.maxcts.shape),
desc='Fitting Spectra',
leave=False):
d.maxcts[m, n], d.peakwl[m, n], d.fwhm[m, n] = fitmethod(
d.wl[~longpass_mask], d.spectra[m, n, ~longpass_mask])
mask = d.maxcts < threshold
d.maxcts[mask] = np.nan
d.fwhm[mask] = np.nan
d.peakwl[mask] = np.nan
d.extent = [d.xpos[0], d.xpos[-1], d.ypos[0], d.ypos[-1]] #map dimensions
return d
def main():
usage_msg = """%(prog)s - convert a wdf file to txt
%(prog)s [OPTION]... [FILE]
Extracts and formats data from a wdf file into multiple txt file.
All txt files will be placed into a single directory.
"""
# Parse arguments
parser = ArgumentParser(usage=usage_msg)
parser.add_argument('file')
parser.add_argument("-o", "--output",
help="set OUTPUT as the output directory")
parser.add_argument("-b", "--base",
help="set BASE as the base name for output files")
parser.add_argument("--no-duplicate",
action="store_true",
help="if specified, causes program to exit if output directory already exists")
parser.add_argument("--keep-path",
action="store_true",
help="if specified, will not strip leading directories when creating output directory")
args = parser.parse_args()
### Further argument parsing ###
# Strip any trailing extensions from path name
no_extension = args.file.split('.')[0]
# Strip any leading directories from path
no_directories = no_extension.split('/')[-1]
# Set base name to stripped file name, if not specified
if args.base is None:
args.base = no_directories
# Set to output directory to stripped file name + "_txt", if not specified
# If keep_path specified, retains any leading directories
if args.output is None:
args.output = (no_extension if args.keep_path else no_directories) + "_wdfout"
# Initialize reader
reader = WDFReader(args.file)
# Create output directory
Path(args.output).mkdir(parents=True, exist_ok=not args.no_duplicate)
# Parse reader
spectra_length = len(reader.spectra)
row, col = 0, 0
# Order of iteration:
# iterate x and y simultaneously
# iterate xdata and spectra simultaneously
# spectra[i][j] where i increments ++, and j increments when i = len
for i in range(reader.capacity):
x = reader.xpos[i]
y = reader.ypos[i]
spectra = reader.spectra[row][col]
# Create file and write line by line
with open('{}/{}__X_{}__Y_{}).txt'.format(args.output, args.base, x.round(4), y.round(4)), 'w') as file:
for j in reversed(range(reader.point_per_spectrum)):
# Format: wavenumber spectra value
file.write('{}\t{}\n'.format(reader.xdata[j], spectra[j]))
# Determine row, col from i
row += 1
if row == spectra_length:
row, col = 0, col + 1
def main():
filename = curdir / "spectra_files" / "mapping.wdf"
reader = WDFReader(filename)
assert reader.measurement_type == 3
wn = reader.xdata
spectra = reader.spectra
print(wn.shape, spectra.shape)
# Test newer API
map_x = reader.xpos
map_y = reader.ypos
map_w = reader.map_info["x_span"]
map_h = reader.map_info["y_span"]
# w and h are the measure in xy coordinates
# Level the spectra
spectra = spectra - np.min(spectra, axis=2, keepdims=True)
peaks_a = peak_in_range(spectra, wn, [1295, 1340])
peaks_b = peak_in_range(spectra, wn, [1350, 1400])
ratio = peaks_a / peaks_b
if plot is True:
# Must provide the format to read the optical image
img = mpimg.imread(reader.img, format="jpg")
img_x0, img_y0 = reader.img_origins
img_w, img_h = reader.img_dimensions
print(reader.img_dimensions)
plt.figure(figsize=(10, 5))
# Left, plot the white light image and rectangle area
plt.subplot(121)
# Show the image with upper origin extent See
# https://matplotlib.org/3.1.1/gallery/text_labels_and_annotations/text_alignment.html
plt.imshow(img,
extent=(img_x0, img_x0 + img_w, img_y0 + img_h, img_y0))
# Add rectangle for marking
r = plt.Rectangle(xy=(map_x.min(), map_y.min()),
width=map_w,
height=map_h,
fill=False)
plt.gca().add_patch(r)
plt.xlabel("Stage X [μm]")
plt.ylabel("Stage Y [μm]")
# Right plot histogram of Peak A/B mapping
plt.subplot(122)
plt.imshow(ratio,
interpolation="bicubic",
extent=[0, map_w, map_h, 0],
vmin=0.5,
vmax=1.5)
plt.xlabel("Mapping x [μm]")
plt.ylabel("Mapping y [μm]")
cb = plt.colorbar()
cb.ax.set_title("Ratio")
plt.tight_layout()
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "map-optical.png", dpi=100)
plt.close()
else:
pass
return
def main():
filename = curdir / "spectra_files" / "streamline.wdf"
reader = WDFReader(filename)
print("Measurement: ", reader.measurement_type)
print("Scan: ", reader.scan_type)
assert reader.measurement_type == 3
assert reader.scan_type == 6
wn = reader.xdata
spectra = reader.spectra
print(wn.shape, spectra.shape)
x = reader.xpos
y = reader.ypos
print(len(x), len(y))
w, h = reader.map_shape
print("The size of mapping is {0:d} * {1:d}".format(w, h))
# w and h are the measure in xy coordinates
# Level the spectra
spectra = spectra - np.min(spectra, axis=2, keepdims=True)
peaks_a = peak_in_range(spectra, wn, [1295, 1340])
peaks_b = peak_in_range(spectra, wn, [1350, 1400])
ratio = peaks_a / peaks_b
ratio_fl = ratio.flatten()
if plot is True:
plt.figure(figsize=(10, 5))
# Left plot histogram of Peak A/B ratio
plt.subplot(121)
img = mpimg.imread(reader.img, format="jpg")
img_x0, img_y0 = reader.img_origins
img_w, img_h = reader.img_dimensions
plt.imshow(img,
extent=(img_x0, img_x0 + img_w, img_y0 + img_h, img_y0))
plt.scatter(x, y, s=0.4, alpha=0.8)
# plt.hist(ratio_fl, bins=50, range=(0.1, 2))
# plt.xlabel("Ratio peak A / peak B")
# plt.ylabel("Counts")
# Right plot histogram of Peak A/B mapping
plt.subplot(122)
plt.imshow(
peaks_b,
interpolation="bicubic",
extent=[0, x.max() - x.min(),
y.max() - y.min(), 0],
)
# vmin=0.5, vmax=1.5)
plt.xlabel("Mapping x [μm]")
plt.ylabel("Mapping y [μm]")
cb = plt.colorbar()
cb.ax.set_title("Signal")
plt.tight_layout()
plt.show(block=False)
plt.pause(3)
plt.savefig(imgdir / "mapping_streamline.png", dpi=100)
plt.close()
else:
pass
return
Raman spectra typically have better signal-to-noise ratios, so there is
not background subtracion performed in this program
"""
from renishawWiRE import WDFReader
import matplotlib.pyplot as plt
# input file path and file name
IN_PATH = r'Z:\Trumann\Renishaw\20210304 PVSe33'
FNAME = r'\PVSe33.4_3 Au side raman map0.wdf'
# import wdf file
filename = IN_PATH+FNAME
reader = WDFReader(filename)
reader.print_info()
# get x-axis of spectral data
# keep in mind the units you specified for the measurement
# here, raman shift (cm-1) was specified and would be the x-axis of the spectrum
shift = reader.xdata
# get the spectral data
# if .wdf file is a map, 'spectra' is 3D (y_pixel, x_pixel, intensity)
# if .wdf file is spot, 'spectra' is 1D (intensity)
# if .wdf file is aborted map, 'spectra' is 2D (y_pix*x_pix, intensity)
spectra = reader.spectra
# check the spectrum of the first pixel
# this will not work if the map was aborted
def main():
usage_msg = """%(prog)s - convert a wdf file to txt
%(prog)s [OPTION]... [FILE]
Extracts and formats data from a wdf file into multiple txt file.
All txt files will be placed into a single directory.
"""
# Parse arguments
parser = ArgumentParser(usage=usage_msg)
parser.add_argument('file')
parser.add_argument("-o",
"--output",
help="set OUTPUT as the output directory")
parser.add_argument("-b",
"--base",
help="set BASE as the base name for output files")
parser.add_argument(
"-p",
"--parent",
help="set PARENT as the parent directory of the output directory")
parser.add_argument(
"--no-duplicate",
action="store_true",
help=
"if specified, causes program to exit if output directory already exists"
)
parser.add_argument(
"--keep-path",
action="store_true",
help=
"if specified, will not strip leading directories when creating output directory"
)
args = parser.parse_args()
### Further argument parsing ###
# Strip any leading directories from path
dir_split = args.file.split('/')
no_dir = dir_split[-1]
# Strip any trailing extension from file
stripped = no_dir.split('.')[0]
# Set base name to stripped file name, if not specified
if args.base is None:
args.base = stripped
# Set to output directory to stripped file name + "_txt", if not specified
# If keep_path specified, will not strip leading directories
if args.keep_path:
dir_split[-1] = ''
stripped = '/'.join(dir_split) + stripped
if args.output is None:
args.output = stripped + "_txt"
# If parent directory specified, make sure to append '/' for proper traversal
# Otherwise, leave blank as to not disrupt relative/absolute pathing
if args.parent is None:
args.parent = ''
else:
args.parent += '/'
dirname = f'{args.parent}{args.output}'
try:
if not Path(args.file).is_file():
# Error: invalid input file
raise Exception(f'invalid input file: {args.file}')
# Initialize reader
try:
reader = WDFReader(args.file)
except Exception as e:
# Error: cannot read file
raise Exception(f'cannot read file: {args.file}')
# Create output directory
directory = Path(dirname)
if directory.exists() and not directory.is_dir():
# Error: existing path is a file
raise Exception(f'output directory is already a file: {dirname}')
if directory.exists() and args.no_duplicate:
# Error: duplicate directory
raise Exception(f'directory already exists: {dirname}')
directory.mkdir(parents=True, exist_ok=not args.no_duplicate)
# Parse reader
spectra_length = len(reader.spectra)
row, col = 0, 0
spectra = reader.spectra.flatten()
start = 0
# Order of iteration:
# iterate x and y simultaneously
# iterate xdata and spectra simultaneously
# spectra[i][j] where i increments ++, and j increments when i = len
for i in range(reader.capacity):
x = reader.xpos[i]
y = reader.ypos[i]
# Create file and write line by line
filename = f'{dirname}/{args.base}__X_{x.round(4)}__Y_{y.round(4)}.txt'
with open(filename, 'w') as file:
for j in range(reader.point_per_spectrum):
# Format: wavenumber spectra value
file.write(
f'{reader.xdata[j]:.6f}\t{spectra[start + j]:.6f}\n')
start += reader.point_per_spectrum
exit(0)
except Exception as e:
print(e, file=sys.stderr)
exit(1)