From 305aa67db56d3fdaba2ce8a49126b9bd0277790c Mon Sep 17 00:00:00 2001
From: Swainlab <peter.swain@ed.ac.uk>
Date: Wed, 17 May 2023 16:19:06 +0100
Subject: [PATCH] minor edits to docs
---
src/postprocessor/core/lineageprocess.py | 2 +-
src/postprocessor/core/processor.py | 50 +++++++++-------------
src/postprocessor/core/reshapers/picker.py | 2 +-
3 files changed, 22 insertions(+), 32 deletions(-)
diff --git a/src/postprocessor/core/lineageprocess.py b/src/postprocessor/core/lineageprocess.py
index 23c75404..b8e3e76b 100644
--- a/src/postprocessor/core/lineageprocess.py
+++ b/src/postprocessor/core/lineageprocess.py
@@ -72,5 +72,5 @@ class LineageProcess(PostProcessABC):
elif self.cells is not None:
lineage = self.cells.mothers_daughters
else:
- raise Exception("No linage information found")
+ raise Exception("No lineage information found")
return lineage
diff --git a/src/postprocessor/core/processor.py b/src/postprocessor/core/processor.py
index 72bbf3f7..42dae83a 100644
--- a/src/postprocessor/core/processor.py
+++ b/src/postprocessor/core/processor.py
@@ -1,3 +1,4 @@
+# change "prepost" to "preprocess"; change filename to postprocessor_engine.py ??
import typing as t
from itertools import takewhile
@@ -61,34 +62,22 @@ class PostProcessorParameters(ParametersABC):
kind: list of str
If "ph_batman" included, add targets for experiments using pHlourin.
"""
- # each subitem specifies the function to be called and the location
- # on the h5 file to be written
+ # each subitem specifies the function to be called
+ # and the h5-file location for the results
+ #: why does merger have a string and picker a list?
targets = {
"prepost": {
"merger": "/extraction/general/None/area",
"picker": ["/extraction/general/None/area"],
},
"processes": [
- [
- "buddings",
- ["/extraction/general/None/volume"],
- ],
- [
- "dsignal",
- [
- "/extraction/general/None/volume",
- ],
- ],
- [
- "bud_metric",
- [
- "/extraction/general/None/volume",
- ],
- ],
+ ["buddings", ["/extraction/general/None/volume"]],
+ ["dsignal", ["/extraction/general/None/volume"]],
+ ["bud_metric", ["/extraction/general/None/volume"]],
[
"dsignal",
[
- "/postprocessing/bud_metric/extraction_general_None_volume",
+ "/postprocessing/bud_metric/extraction_general_None_volume"
],
],
],
@@ -129,7 +118,7 @@ class PostProcessorParameters(ParametersABC):
class PostProcessor(ProcessABC):
def __init__(self, filename, parameters):
"""
- Initialise PostProcessor
+ Initialise PostProcessor.
Parameters
----------
@@ -172,31 +161,32 @@ class PostProcessor(ProcessABC):
self.targets = parameters["targets"]
def run_prepost(self):
- """Using picker, get and write lineages, returning mothers and daughters."""
- """Important processes run before normal post-processing ones"""
+ """
+ Run picker and merger and get lineages.
+
+ Necessary before any processes can run.
+ """
+ # run merger
record = self._signal.get_raw(self.targets["prepost"]["merger"])
merges = np.array(self.merger.run(record), dtype=int)
-
self._writer.write(
"modifiers/merges", data=[np.array(x) for x in merges]
)
-
+ # get lineages from picker
lineage = _assoc_indices_to_3d(self.picker.cells.mothers_daughters)
lineage_merged = []
-
- if merges.any(): # Update lineages after merge events
-
+ if merges.any():
+ # update lineages after merge events
merged_indices = merge_association(lineage, merges)
- # Remove repeated labels post-merging
+ # remove repeated labels post-merging
lineage_merged = np.unique(merged_indices, axis=0)
-
self.lineage = _3d_index_to_2d(
lineage_merged if len(lineage_merged) else lineage
)
self._writer.write(
"modifiers/lineage_merged", _3d_index_to_2d(lineage_merged)
)
-
+ # run picker
picked_indices = self.picker.run(
self._signal[self.targets["prepost"]["picker"][0]]
)
diff --git a/src/postprocessor/core/reshapers/picker.py b/src/postprocessor/core/reshapers/picker.py
index 56bace44..e6d8b598 100644
--- a/src/postprocessor/core/reshapers/picker.py
+++ b/src/postprocessor/core/reshapers/picker.py
@@ -41,7 +41,7 @@ class Picker(LineageProcess):
parameters: PickerParameters,
cells: Cells or None = None,
):
- """Initialise from a Cells instance."""
+ """Initialise picker."""
super().__init__(parameters=parameters)
self.cells = cells
--
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