From f835dc1377944d3fa2ee1f55532c603ef53b0110 Mon Sep 17 00:00:00 2001
From: Eduardo Gonzalez Solares <eglez@ast.cam.ac.uk>
Date: Fri, 10 May 2019 13:59:53 +0100
Subject: [PATCH] Add function to parse mocasic file
---
stpt_pipeline/mosaic_functions.py | 21 +++++++++++++++++++++
stpt_pipeline/preprocess.py | 14 +++++++-------
2 files changed, 28 insertions(+), 7 deletions(-)
diff --git a/stpt_pipeline/mosaic_functions.py b/stpt_pipeline/mosaic_functions.py
index 6af9e3f..609a6eb 100644
--- a/stpt_pipeline/mosaic_functions.py
+++ b/stpt_pipeline/mosaic_functions.py
@@ -1,4 +1,6 @@
from os import listdir
+from pathlib import Path
+from typing import Dict
import dask.array as da
import numpy as np
@@ -111,6 +113,25 @@ def get_mosaic_file(root_dir):
return ''
+def parse_mosaic_file(root_dir: Path) -> Dict[str, str]:
+ """Return contents of mosaic file as dictionary.
+
+ Parameters
+ ----------
+ root_dir
+ Directory containing mosaic file
+
+ Returns
+ -------
+ dictionary of key, values with mosaic file contents
+ """
+ mosaic_file = get_mosaic_file(root_dir)
+ with open(mosaic_file) as fh:
+ items = [item.strip().split(':', 1) for item in fh.readlines()]
+ res = {k[0]: k[1] for k in items}
+ return res
+
+
def get_img_cube(
root_dir,
imgs,
diff --git a/stpt_pipeline/preprocess.py b/stpt_pipeline/preprocess.py
index 046b83b..2125ab9 100644
--- a/stpt_pipeline/preprocess.py
+++ b/stpt_pipeline/preprocess.py
@@ -8,15 +8,17 @@ import zarr
from dask import delayed
from distributed import Client, wait
from scipy.ndimage import geometric_transform
+from zarr import blosc
from imaxt_image.image import TiffImage
from stpt_pipeline.utils import get_coords
-from .mosaic_functions import get_mosaic_file
+from .mosaic_functions import parse_mosaic_file
from .settings import Settings
from .stpt_displacement import defringe, magic_function
log = logging.getLogger('owl.daemon.pipeline')
+blosc.use_threads = False # TODO: Check if this makes it quicker or slower
def read_flatfield(flat_file: Path):
@@ -141,14 +143,11 @@ def preprocess(root_dir: Path, flat_file: Path, output_dir: Path):
z = zarr.group(out, 'w')
dirs = list_directories(root_dir)
- for d in dirs:
+ for d in dirs[:2]:
# TODO: All this should be metadata
section = re.compile(r'\d\d\d\d$').search(d.name).group()
- mosaic_file = get_mosaic_file(d)
- res = open(d / mosaic_file, 'r').read()
- mrows = re.compile(r'mrows:(\d+)\n').search(res).groups()[0]
- mcolumns = re.compile(r'mcolumns:(\d+)\n').search(res).groups()[0]
- mrows, mcolumns = int(mrows), int(mcolumns)
+ mosaic = parse_mosaic_file(d)
+ mrows, mcolumns = int(mosaic['mrows']), int(mosaic['mcolumns'])
fovs = mrows * mcolumns
files = sorted(list(d.glob('*.tif')))
files_ch1 = sorted(list(d.glob('*_01.tif')))
@@ -168,6 +167,7 @@ def preprocess(root_dir: Path, flat_file: Path, output_dir: Path):
wait(fut)
# Write metadata
+ # TODO: Write contents of mosaic file here as well
z.attrs['sections'] = len(dirs) # TODO: Read from mosaic file
z.attrs['fovs'] = fovs
z.attrs['mrows'] = mrows
--
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