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- save pdf with some plots

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- calculate offset time for each carpet
- globbing for Windows
- close files when needed
- skip carpets and plots for files without track
This commit is contained in:
Wim Pomp
2022-11-21 14:07:54 +01:00
parent 21b0d81e8d
commit 5afa20b78a
3 changed files with 98 additions and 16 deletions
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2
.gitignore vendored
View File

@@ -130,3 +130,5 @@ dmypy.json
# PyCharm
.idea/
/issfile/_version.py

95
issfile/__init__.py
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@@ -2,6 +2,8 @@ import re
import pickle
import xml.etree.ElementTree as ET
import numpy as np
from glob import glob
from pathlib import Path
from zipfile import ZipFile
from struct import unpack
from tiffwrite import IJTiffFile, Tag
@@ -9,6 +11,10 @@ from tqdm.auto import tqdm
from itertools import product
from yaml import safe_load
from argparse import ArgumentParser
from atexit import register
from matplotlib import pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from ._version import __version__, __git_commit_hash__
class TiffFile(IJTiffFile):
@@ -39,6 +45,12 @@ class TiffFile(IJTiffFile):
frame = self.iss.get_image(*frame[1:])
return super().compress_frame(frame.astype(self.dtype))
def clean(self):
try:
self.iss.close()
except Exception:
pass
class IssFile:
def __init__(self, file, version=388):
@@ -57,7 +69,8 @@ class IssFile:
self.exposure_time = float(self.metadata.find('FrameIntervalTime').text)
self.pxsize = float(self.metadata.find('Boundary').find('FrameWidth').text) / self.shape[0]
self.alba_metadata = safe_load('\n'.join([IssFile.parse_line(line)
for line in self.metadata.find('AlbaSystemSettings').find('withComments').text.splitlines()]))
for line in self.metadata.find('AlbaSystemSettings')
.find('withComments').text.splitlines()]))
particle_tracking = self.alba_metadata['ParticleTracking']
self.points_per_orbit = particle_tracking['ScanCirclePointCount']
self.orbits_per_cycle = particle_tracking['OrbitCountPerTrack']
@@ -67,6 +80,7 @@ class IssFile:
self.data_bytes_len = self.zip.getinfo('data/PrimaryDecayData.bin').file_size
self.delta = self.data_bytes_len // (self.shape[0] * self.shape[1] * self.shape[2] *
(self.shape[3] + self.shape[4]))
self._carpet_t0 = [0]
def __enter__(self):
return self
@@ -81,6 +95,7 @@ class IssFile:
self.__dict__.update(state)
self.zip = ZipFile(self.file)
self.data = self.zip.open('data/PrimaryDecayData.bin')
register(self.close)
def close(self):
try:
@@ -121,21 +136,31 @@ class IssFile:
index = np.zeros(int(round(max(metadata[:, 0]) / self.cycle_time)) + 1, int)
for i, j in enumerate(metadata[:, 0]):
index[int(round(j / self.cycle_time))] = i
metadata[:, 0] += self.get_carpet_t0(t, metadata.shape[0])
return data[index], metadata[index].T
def get_carpet_t0(self, t, cycles=None):
if t + 1 > len(self._carpet_t0):
cycles = cycles or self.get_carpet(0, t - 1)[1].shape[1]
t0 = self.get_carpet_t0(t - 1)
self._carpet_t0.append(t0 + cycles * self.cycle_time + self.exposure_time)
return self._carpet_t0[t]
def save_images_as_tiff(self, file):
with tqdm(total=self.shape[2] * self.shape[3], desc='Writing images') as bar:
with TiffFile(file, (self.shape[2], 1, self.shape[3]), iss=self, bar=bar,
pxsize=self.pxsize, comment=ET.tostring(self.metadata)) as tif:
for c, t in product(range(self.shape[2]), range(self.shape[3])):
tif.save(np.array((0, c, t)), c, 0, t)
if self.shape[3]:
with tqdm(total=self.shape[2] * self.shape[3], desc='Writing images') as bar:
with TiffFile(file, (self.shape[2], 1, self.shape[3]), iss=self, bar=bar,
pxsize=self.pxsize, comment=ET.tostring(self.metadata)) as tif:
for c, t in product(range(self.shape[2]), range(self.shape[3])):
tif.save((0, c, t), c, 0, t)
def save_carpets_as_tiff(self, file):
with tqdm(total=self.shape[2] * self.shape[4], desc='Writing carpets') as bar:
with TiffFile(file, (self.shape[2], 1, self.shape[4]), iss=self, bar=bar,
pxsize=self.orbit_pxsize, comment=ET.tostring(self.metadata)) as tif:
for c, t in product(range(self.shape[2]), range(self.shape[4])):
tif.save(np.array((1, c, t)), c, 0, t)
if self.shape[4]:
with tqdm(total=self.shape[2] * self.shape[4], desc='Writing carpets') as bar:
with TiffFile(file, (self.shape[2], 1, self.shape[4]), iss=self, bar=bar,
pxsize=self.orbit_pxsize, comment=ET.tostring(self.metadata)) as tif:
for c, t in product(range(self.shape[2]), range(self.shape[4])):
tif.save((1, c, t), c, 0, t)
@staticmethod
def parse_line(line):
@@ -146,6 +171,47 @@ class IssFile:
line = re.sub(r'\s*=\s*', r' ', line)
return line
def get_txyzi(self, c):
data, metadata = zip(*[self.get_carpet(c, t) for t in range(self.shape[4])])
txyz = np.hstack(metadata)
idx = np.all(txyz[1:] != 0, 0)
return *txyz[:, idx], np.hstack([d.sum(1) for d in data])[idx]
def save_plot(self, file):
if self.shape[4]:
with PdfPages(file) as pdf:
plt.figure(figsize=(8.3, 11.7))
plt.subplot(3, 1, 1)
for c, color in zip(range(self.shape[2]), 'rgbm'):
t, x, y, z, intensity = self.get_txyzi(c)
plt.plot(t / 1000, intensity, color)
plt.xlabel('time (s)')
plt.ylabel('sum intensity (counts)')
plt.legend([f'channel {i}' for i in range(self.shape[2])])
plt.subplot(3, 1, 2)
for i, color in zip((x, y, z), 'rgb'):
plt.plot(t / 1000, i, color)
plt.xlabel('time (s)')
plt.ylabel('position (μm)')
plt.legend('xyz')
plt.subplot(3, 3, 7)
plt.plot(x, y, 'k')
plt.axis('equal')
plt.xlabel('x (μm)')
plt.ylabel('y (μm)')
plt.subplot(3, 3, 8)
plt.plot(x, z, 'k')
plt.axis('equal')
plt.xlabel('x (μm)')
plt.ylabel('z (μm)')
plt.subplot(3, 3, 9)
plt.plot(y, z, 'k')
plt.axis('equal')
plt.xlabel('y (μm)')
plt.ylabel('z (μm)')
plt.tight_layout()
pdf.savefig()
def main():
parser = ArgumentParser(description='Convert .iss-pt files into .tiff files.')
@@ -154,10 +220,11 @@ def main():
help='version of VistaVision with which the .iss-pt was written, default: 388')
args = parser.parse_args()
for file in args.files:
for file in [Path(file) for files in args.files for file in glob(files)]:
with IssFile(file, args.version) as iss_file:
iss_file.save_images_as_tiff(file.replace('.iss-pt', '.tif'))
iss_file.save_carpets_as_tiff(file.replace('.iss-pt', '.carpet.tif'))
iss_file.save_images_as_tiff(file.with_suffix('.tif'))
iss_file.save_carpets_as_tiff(file.with_suffix('.carpet.tif'))
iss_file.save_plot(file.with_suffix('.pdf'))
if __name__ == '__main__':

17
setup.py
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@@ -1,11 +1,24 @@
import os
import setuptools
version = '2022.11.0'
with open('README.md', 'r') as fh:
long_description = fh.read()
with open(os.path.join(os.path.dirname(__file__), 'issfile', '_version.py'), 'w') as f:
f.write(f"__version__ = '{version}'\n")
try:
with open(os.path.join(os.path.dirname(__file__), '.git', 'HEAD')) as g:
head = g.read().split(':')[1].strip()
with open(os.path.join(os.path.dirname(__file__), '.git', head)) as h:
f.write("__git_commit_hash__ = '{}'\n".format(h.read().rstrip('\n')))
except Exception:
f.write(f"__git_commit_hash__ = 'unknown'\n")
setuptools.setup(
name='issfile',
version='2022.10.4',
version=version,
author='Wim Pomp @ Lenstra lab NKI',
author_email='w.pomp@nki.nl',
description='Open ISS files.',
@@ -19,6 +32,6 @@ setuptools.setup(
'Operating System :: OS Independent',
],
python_requires='>=3.8',
install_requires=['numpy', 'tqdm', 'pyyaml', 'tiffwrite>=2022.10.2'],
install_requires=['numpy', 'matplotlib', 'tqdm', 'pyyaml', 'tiffwrite>=2022.10.2'],
entry_points={'console_scripts': ['iss2tiff=issfile:main']}
)