diff --git a/docs/source/specifications/metadata.org b/docs/source/specifications/metadata.org
index 139faf2def930e3b3c3c092c85e401c75d32f7ff..52d514a3465236a9079a8bba3ee721b013808a28 100644
--- a/docs/source/specifications/metadata.org
+++ b/docs/source/specifications/metadata.org
@@ -4,7 +4,7 @@ Draft for recommended metadata for images to provide a standard interface for al
* Essential data
- DimensionOrder: str
- Order of dimensions (e.g., TCZYX for Channel, Time, Z,X,Y)
+ Order of dimensions (e.g., TCZYX for Time, Channel, Z, Y, X)
- PixelSize: float
Size of pixel, useful for segmentation.
- Channels: List[str]
diff --git a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif
index f813c15a9c8aef8a6e629ff17e460aef4acdb630..569f33a72ab18f65c79e28e38869a4f17cd30cca 100755
Binary files a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif and b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003.tif differ
diff --git a/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif
new file mode 100755
index 0000000000000000000000000000000000000000..f813c15a9c8aef8a6e629ff17e460aef4acdb630
Binary files /dev/null and b/examples/tiler/pypipeline_unit_test_00_000001_Brightfield_003_square.tif differ
diff --git a/src/agora/abc.py b/src/agora/abc.py
index 6c1fd343e04bf42fb798642484b0b55c2de0a97a..c396b4b1503c7558dc51eaf9032b7cb14485bc38 100644
--- a/src/agora/abc.py
+++ b/src/agora/abc.py
@@ -10,6 +10,8 @@ from typing import Union
from flatten_dict import flatten
from yaml import dump, safe_load
+from agora.logging import timer
+
atomic = t.Union[int, float, str, bool]
@@ -239,21 +241,12 @@ class StepABC(ProcessABC):
def _run_tp(self):
pass
- def run_tp(self, tp: int, log: bool = True, **kwargs):
+ @timer
+ def run_tp(self, tp: int, **kwargs):
"""
Time and log the timing of a step.
"""
- if log:
- t = perf_counter()
- result = self._run_tp(tp, **kwargs)
- self._log(
- f"Timing:{self.__class__.__name__}:{perf_counter()-t}s",
- "debug",
- )
- else:
- result = self._run_tp(tp, **kwargs)
-
- return result
+ return self._run_tp(tp, **kwargs)
def run(self):
# Replace run withn run_tp
diff --git a/src/agora/io/metadata.py b/src/agora/io/metadata.py
index 61caa3aa6c868f33a0f40ce220a02d3a3d028285..c058e9f430672a9fc4cb6a7e25d4e328368a2044 100644
--- a/src/agora/io/metadata.py
+++ b/src/agora/io/metadata.py
@@ -168,8 +168,9 @@ def get_meta_swainlab(parsed_metadata: dict):
def get_meta_from_legacy(parsed_metadata: dict):
- channels = parsed_metadata["channels/channel"]
- return {"channels": channels}
+ result = parsed_metadata
+ result["channels"] = result["channels/channel"]
+ return result
def parse_swainlab_metadata(filedir: t.Union[str, PosixPath]):
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 1b174089ba5f176cdfb1a90be5fc7a16666ce243..0210ef3427552c8d7fa62a9f366976459d112e51 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -84,7 +84,7 @@ class Signal(BridgeH5):
try:
df.columns = (df.columns * self.tinterval // 60).astype(int)
except Exception as e:
- self._log(f"Unable to convert columns to minutes: {e}")
+ self._log(f"Unable to convert columns to minutes: {e}", "debug")
return df
@cached_property
diff --git a/src/agora/io/writer.py b/src/agora/io/writer.py
index bc8769a2ec44e5c3ff4bead42d0fdec53ea20ad1..264478482875c6992241ed9ad00613f0ef96fbf0 100644
--- a/src/agora/io/writer.py
+++ b/src/agora/io/writer.py
@@ -1,4 +1,3 @@
-import itertools
import logging
from collections.abc import Iterable
from pathlib import Path
@@ -55,6 +54,11 @@ class DynamicWriter:
if Path(file).exists():
self.metadata = load_attributes(file)
+ def _log(self, message: str, level: str = "warn"):
+ # Log messages in the corresponding level
+ logger = logging.getLogger("aliby")
+ getattr(logger, level)(f"{self.__class__.__name__}: {message}")
+
def _append(self, data, key, hgroup):
"""
Append data to existing dataset in the h5 file otherwise create a new one.
@@ -170,7 +174,9 @@ class DynamicWriter:
self._append(value, key, hgroup)
except Exception as e:
print(key, value)
- raise (e)
+ self._log(
+ f"{key}:{value} could not be written: {e}", "error"
+ )
# write metadata
for key, value in meta.items():
hgroup.attrs[key] = value
@@ -564,7 +570,7 @@ class Writer(BridgeH5):
dset[()] = df.index.get_level_values(level=name).tolist()
# create dataset and write columns
if (
- df.columns.dtype == np.int
+ df.columns.dtype == int
or df.columns.dtype == np.dtype("uint")
or df.columns.name == "timepoint"
):
@@ -601,9 +607,7 @@ class Writer(BridgeH5):
)
# split indices in existing and additional
new = df.index.tolist()
- if (
- df.index.nlevels == 1
- ):
+ if df.index.nlevels == 1:
# cover cases with a single index
new = [(x,) for x in df.index.tolist()]
(
diff --git a/src/agora/logging.py b/src/agora/logging.py
new file mode 100644
index 0000000000000000000000000000000000000000..a004b0182363d495c32ffcb2edf9d51cd8875303
--- /dev/null
+++ b/src/agora/logging.py
@@ -0,0 +1,20 @@
+#!/usr/bin/env jupyter
+"""
+Add general logging functions and decorators
+"""
+
+import logging
+from time import perf_counter
+
+
+def timer(func):
+ # Log duration of a function into aliby logfile
+ def wrap_func(*args, **kwargs):
+ t1 = perf_counter()
+ result = func(*args, **kwargs)
+ logging.getLogger("aliby").debug(
+ f"{func.__qualname__} took {(perf_counter()-t1):.4f}s"
+ )
+ return result
+
+ return wrap_func
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 0062c61a75b96e2fe112f1cad2b637a842d19d49..f7f47cfb316bde17a6aad3a1abc6568f9397c294 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -475,7 +475,7 @@ class Pipeline(ProcessABC):
step == "tiler"
and i == min_process_from
):
- print(
+ logging.getLogger("aliby").info(
f"Found {steps['tiler'].n_traps} traps in {image.name}"
)
elif (
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index a3216e9eb7f0987238161a977249b4c74a1bb4dc..34aa89d1c2af76976f134a0fd38d58919cedc9bb 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -261,14 +261,13 @@ class Tiler(StepABC):
"""
imgdmy_obj = ImageDummy(parameters)
dummy_image = imgdmy_obj.get_data_lazy()
- dummy_omero_metadata = ( # Default to "tczyx" if image.dimorder is None
- {
- f"size_{dim}": dim_size
- for dim, dim_size in zip(
- imgdmy_obj.dimorder or "tczyx", dummy_image.shape
- )
- },
- )
+ # Default to "tczyx" if image.dimorder is None
+ dummy_omero_metadata = {
+ f"size_{dim}": dim_size
+ for dim, dim_size in zip(
+ imgdmy_obj.dimorder or "tczyx", dummy_image.shape
+ )
+ }
dummy_omero_metadata.update(
{
"channels": [