From 0feb0543de35888b079cca71a28704c2e8a97323 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Fri, 6 Oct 2023 17:21:07 +0100
Subject: [PATCH] tidying: deleted phlourin bits from processor
---
src/aliby/pipeline.py | 5 ++-
src/postprocessor/core/abc.py | 4 +--
src/postprocessor/core/processor.py | 56 +++++++----------------------
3 files changed, 18 insertions(+), 47 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index d80f441c..f373702c 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -324,6 +324,9 @@ class Pipeline(ProcessABC):
directory.mkdir(parents=True)
# download logs to use for metadata
conn.cache_logs(directory)
+ print("Positions available:")
+ for i, pos in enumerate(position_ids.keys()):
+ print("\t" + f"{i}: " + pos.split(".")[0])
# update configuration
self.parameters.general["directory"] = str(directory)
config["general"]["directory"] = directory
@@ -341,7 +344,7 @@ class Pipeline(ProcessABC):
if not len(position_ids):
raise Exception("No images to segment.")
else:
- print("Positions:")
+ print("\nPositions selected:")
for pos in position_ids:
print("\t" + pos.split(".")[0])
# create and run pipelines
diff --git a/src/postprocessor/core/abc.py b/src/postprocessor/core/abc.py
index addeb031..73cf1089 100644
--- a/src/postprocessor/core/abc.py
+++ b/src/postprocessor/core/abc.py
@@ -46,18 +46,16 @@ def get_process(process, suffix="") -> PostProcessABC or ParametersABC or None:
_to_snake_case(process),
_to_pascal_case(_to_snake_case(process)),
)
-
found = None
for possible_location, process_syntax in product(
possible_locations, valid_syntaxes
):
-
location = f"{base_location}.{possible_location}.{_to_snake_case(process)}.{process_syntax}{suffix}"
+ # instantiate class but not a class object
found = locate(location)
if found is not None:
break
else:
-
raise Exception(
f"{process} not found in locations {possible_locations} at {base_location}"
)
diff --git a/src/postprocessor/core/processor.py b/src/postprocessor/core/processor.py
index 6bf1372c..008b6ebf 100644
--- a/src/postprocessor/core/processor.py
+++ b/src/postprocessor/core/processor.py
@@ -72,14 +72,7 @@ class PostProcessorParameters(ParametersABC):
},
"processes": [
["buddings", ["/extraction/general/None/volume"]],
- # ["dsignal", ["/extraction/general/None/volume"]],
["bud_metric", ["/extraction/general/None/volume"]],
- # [
- # "dsignal",
- # [
- # "/postprocessing/bud_metric/extraction_general_None_volume"
- # ],
- # ],
],
}
param_sets = {
@@ -89,29 +82,6 @@ class PostProcessorParameters(ParametersABC):
}
}
outpaths = {}
- outpaths["aggregate"] = "/postprocessing/experiment_wide/aggregated/"
- # pHlourin experiments are special
- if "ph_batman" in kind:
- targets["processes"]["dsignal"].append(
- [
- "/extraction/em_ratio/np_max/mean",
- "/extraction/em_ratio/np_max/median",
- "/extraction/em_ratio_bgsub/np_max/mean",
- "/extraction/em_ratio_bgsub/np_max/median",
- ]
- )
- targets["processes"]["aggregate"].append(
- [
- [
- "/extraction/em_ratio/np_max/mean",
- "/extraction/em_ratio/np_max/median",
- "/extraction/em_ratio_bgsub/np_max/mean",
- "/extraction/em_ratio_bgsub/np_max/median",
- "/extraction/gsum/np_max/median",
- "/extraction/gsum/np_max/mean",
- ]
- ],
- )
return cls(targets=targets, param_sets=param_sets, outpaths=outpaths)
@@ -128,9 +98,9 @@ class PostProcessor(ProcessABC):
An instance of PostProcessorParameters.
"""
super().__init__(parameters)
- self._filename = filename
- self._signal = Signal(filename)
- self._writer = Writer(filename)
+ self.filename = filename
+ self.signal = Signal(filename)
+ self.writer = Writer(filename)
# parameters for merger and picker
dicted_params = {
i: parameters["param_sets"]["prepost"][i]
@@ -167,7 +137,7 @@ class PostProcessor(ProcessABC):
Necessary before any processes can run.
"""
# run merger
- record = self._signal.get_raw(self.targets["prepost"]["merger"])
+ record = self.signal.get_raw(self.targets["prepost"]["merger"])
merges = self.merger.run(record)
# get lineages from picker
lineage = _assoc_indices_to_3d(self.picker.cells.mothers_daughters)
@@ -178,18 +148,18 @@ class PostProcessor(ProcessABC):
new_lineage = lineage
new_merges = merges
self.lineage = _3d_index_to_2d(new_lineage)
- self._writer.write(
+ self.writer.write(
"modifiers/merges", data=[np.array(x) for x in new_merges]
)
- self._writer.write(
+ self.writer.write(
"modifiers/lineage_merged", _3d_index_to_2d(new_lineage)
)
# run picker
picked_indices = self.picker.run(
- self._signal[self.targets["prepost"]["picker"][0]]
+ self.signal[self.targets["prepost"]["picker"][0]]
)
if picked_indices.any():
- self._writer.write(
+ self.writer.write(
"modifiers/picks",
data=pd.MultiIndex.from_arrays(
picked_indices.T, names=["trap", "cell_label"]
@@ -213,9 +183,9 @@ class PostProcessor(ProcessABC):
self.parameters[process]
)
else:
- # assign parameters
+ # assign default parameters
parameters = self.parameters_classfun[process].default()
- # load process
+ # load process - instantiate an object in the class
loaded_process = self.classfun[process](parameters)
if isinstance(parameters, LineageProcessParameters):
loaded_process.lineage = self.lineage
@@ -227,9 +197,9 @@ class PostProcessor(ProcessABC):
"""Run process to obtain a single dataset and write the result."""
# get pre-processed data
if isinstance(dataset, list):
- signal = [self._signal[d] for d in dataset]
+ signal = [self.signal[d] for d in dataset]
elif isinstance(dataset, str):
- signal = self._signal[dataset]
+ signal = self.signal[dataset]
else:
raise ("Incorrect dataset")
# run process on signal
@@ -292,7 +262,7 @@ class PostProcessor(ProcessABC):
result: t.Union[t.List, pd.DataFrame, np.ndarray],
metadata: t.Dict,
):
- self._writer.write(path, result, meta=metadata, overwrite="overwrite")
+ self.writer.write(path, result, meta=metadata, overwrite="overwrite")
@staticmethod
def pick_mother(a, b):
--
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