From cbe8a5ae9f3d764ad020da96dabfdc76f7f8cb39 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 17 Oct 2019 14:20:16 +0200
Subject: [PATCH] Update intensity correction scripts
---
analysis/correct_intensities.py | 48 +++++++++++++++++++++------
example_updates/update_major_100.json | 2 +-
2 files changed, 39 insertions(+), 11 deletions(-)
diff --git a/analysis/correct_intensities.py b/analysis/correct_intensities.py
index 250e788..37d5664 100644
--- a/analysis/correct_intensities.py
+++ b/analysis/correct_intensities.py
@@ -6,11 +6,13 @@ from concurrent import futures
import numpy as np
import z5py
import h5py
+import luigi
import vigra
from scipy.ndimage.morphology import binary_dilation
from scripts.transformation import intensity_correction
-from pybdv import make_bdv, convert_to_bdv
+from pybdv import make_bdv
+from pybdv.metadata import write_h5_metadata
def combine_mask():
@@ -113,16 +115,42 @@ def check_chunks():
json.dump(results, f)
+# TODO write hdf5 meta-data
def make_subsampled_volume():
+ from cluster_tools.copy_volume import CopyVolumeLocal
+ task = CopyVolumeLocal
p = './em-raw-wholecorrected.h5'
- k = 't00000/s00/2/cells'
- with h5py.File(p, 'r') as f:
- print(f[k].shape)
- # return
- scale_factors = [[2, 2, 2]] * 6
- convert_to_bdv(p, k, 'em-raw-small-corrected.h5', downscale_factors=scale_factors, downscale_mode='mean',
- resolution=[.05, .04, .04], unit='micrometer')
+ glob_conf = task.default_global_config()
+ task_conf = task.default_task_config()
+
+ tmp_folder = './tmp_copy'
+ config_dir = os.path.join(tmp_folder, 'configs')
+ os.makedirs(config_dir, exist_ok=True)
+
+ out_path = 'em-raw-small-corrected.h5'
+
+ shebang = '/g/kreshuk/pape/Work/software/conda/miniconda3/envs/cluster_env37/bin/python'
+ block_shape = [64, 512, 512]
+ chunks = [32, 256, 256]
+ glob_conf.update({'shebang': shebang, 'block_shape': block_shape})
+ task_conf.update({'threads_per_job': 32, 'chunks': chunks})
+ with open(os.path.join(config_dir, 'global.config'), 'w') as f:
+ json.dump(glob_conf, f)
+ with open(os.path.join(config_dir, 'copy_volume.config'), 'w') as f:
+ json.dump(task_conf, f)
+ for scale in range(5):
+ pref = 's%i' % scale
+ in_key = 't00000/s00/%i/cells' % (scale + 3,)
+ out_key = 't00000/s00/%i/cells' % scale
+ t = task(tmp_folder=tmp_folder, config_dir=config_dir,
+ max_jobs=1, input_path=p, input_key=in_key,
+ output_path=out_path, output_key=out_key,
+ prefix=pref)
+ luigi.build([t], local_scheduler=True)
+
+ scale_factors = 5 * [[2, 2, 2]]
+ write_h5_metadata(out_path, scale_factors)
def make_extrapolation_mask():
@@ -158,5 +186,5 @@ def make_extrapolation_mask():
if __name__ == '__main__':
# correct_intensities('slurm', 125)
- # make_subsampled_volume()
- make_extrapolation_mask()
+ make_subsampled_volume()
+ # make_extrapolation_mask()
diff --git a/example_updates/update_major_100.json b/example_updates/update_major_100.json
index 0aa6d2f..6694b2b 100644
--- a/example_updates/update_major_100.json
+++ b/example_updates/update_major_100.json
@@ -1 +1 @@
-{"xray-6dpf-1-whole" : [{"name": "bla", "input_path": "/path/to/some.xml"}, {}]}
+{"xray-6dpf-1-whole" : [{"name": "raw", "input_path": "/g/schwab/Hamburg XIMG/Registration_xray to sbem/Platy-90_02_registration_1-ch0.xml"}]}
--
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