From 85a66bb2b1e87821836c6daad3cb9b499e8c6461 Mon Sep 17 00:00:00 2001
From: Swainlab <peter.swain@ed.ac.uk>
Date: Fri, 11 Aug 2023 20:26:59 +0100
Subject: [PATCH] added moment_of_inertia to cell functions
---
src/aliby/pipeline.py | 26 +++++++-------
src/extraction/core/functions/cell.py | 36 +++++++++++++++++++
.../core/functions/custom/localisation.py | 5 +--
src/extraction/core/functions/loaders.py | 4 +--
4 files changed, 54 insertions(+), 17 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index c31d0fc2..e5d5bc66 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -126,7 +126,7 @@ class PipelineParameters(ParametersABC):
use_explog=True,
)
}
- # update default values using inputs
+ # update default values for general using inputs
for k, v in general.items():
if k not in defaults["general"]:
defaults["general"][k] = v
@@ -306,7 +306,7 @@ class Pipeline(ProcessABC):
# extract from configuration
expt_id = config["general"]["id"]
distributed = config["general"]["distributed"]
- pos_filter = config["general"]["filter"]
+ position_filter = config["general"]["filter"]
root_dir = Path(config["general"]["directory"])
self.server_info = {
k: config["general"].get(k)
@@ -329,15 +329,15 @@ class Pipeline(ProcessABC):
config["general"]["directory"] = directory
self.setLogger(directory)
# pick particular positions if desired
- if pos_filter is not None:
- if isinstance(pos_filter, list):
+ if position_filter is not None:
+ if isinstance(position_filter, list):
position_ids = {
k: v
- for filt in pos_filter
+ for filt in position_filter
for k, v in self.apply_filter(position_ids, filt).items()
}
else:
- position_ids = self.apply_filter(position_ids, pos_filter)
+ position_ids = self.apply_filter(position_ids, position_filter)
if not len(position_ids):
raise Exception("No images to segment.")
# create and run pipelines
@@ -356,26 +356,26 @@ class Pipeline(ProcessABC):
]
return results
- def apply_filter(self, position_ids: dict, pos_filter: int or str):
+ def apply_filter(self, position_ids: dict, position_filter: int or str):
"""
Select positions.
- Either pick a particular one or use a regular expression to parse
- their file names.
+ Either pick a particular position or use a regular expression
+ to parse their file names.
"""
- if isinstance(pos_filter, str):
+ if isinstance(position_filter, str):
# pick positions using a regular expression
position_ids = {
k: v
for k, v in position_ids.items()
- if re.search(pos_filter, k)
+ if re.search(position_filter, k)
}
- elif isinstance(pos_filter, int):
+ elif isinstance(position_filter, int):
# pick a particular position
position_ids = {
k: v
for i, (k, v) in enumerate(position_ids.items())
- if i == pos_filter
+ if i == position_filter
}
return position_ids
diff --git a/src/extraction/core/functions/cell.py b/src/extraction/core/functions/cell.py
index 0e7b9fe8..4d97f23a 100644
--- a/src/extraction/core/functions/cell.py
+++ b/src/extraction/core/functions/cell.py
@@ -193,3 +193,39 @@ def min_maj_approximation(cell_mask) -> t.Tuple[int]:
# + distance from the center of cone top to edge of cone top
maj_ax = np.round(np.max(dn) + np.sum(cone_top) / 2)
return min_ax, maj_ax
+
+
+def moment_of_inertia(cell_mask, trap_image):
+ """
+ Find moment of inertia - a measure of homogeneity.
+
+ From iopscience.iop.org/article/10.1088/1742-6596/1962/1/012028
+ which cites ieeexplore.ieee.org/document/1057692.
+ """
+ # set pixels not in cell to zero
+ trap_image[~cell_mask] = 0
+ x = trap_image
+ if np.any(x):
+ # x-axis : column=x-axis
+ columnvec = np.arange(1, x.shape[1] + 1, 1)[:, None].T
+ # y-axis : row=y-axis
+ rowvec = np.arange(1, x.shape[0] + 1, 1)[:, None]
+ # find raw moments
+ M00 = np.sum(x)
+ M10 = np.sum(np.multiply(x, columnvec))
+ M01 = np.sum(np.multiply(x, rowvec))
+ # find centroid
+ Xm = M10 / M00
+ Ym = M01 / M00
+ # find central moments
+ Mu00 = M00
+ Mu20 = np.sum(np.multiply(x, (columnvec - Xm) ** 2))
+ Mu02 = np.sum(np.multiply(x, (rowvec - Ym) ** 2))
+ # find invariants
+ Eta20 = Mu20 / Mu00 ** (1 + (2 + 0) / 2)
+ Eta02 = Mu02 / Mu00 ** (1 + (0 + 2) / 2)
+ # find moments of inertia
+ moi = Eta20 + Eta02
+ return moi
+ else:
+ return np.nan
diff --git a/src/extraction/core/functions/custom/localisation.py b/src/extraction/core/functions/custom/localisation.py
index 07c22587..08f034e8 100644
--- a/src/extraction/core/functions/custom/localisation.py
+++ b/src/extraction/core/functions/custom/localisation.py
@@ -1,8 +1,9 @@
-""" How to do the nuc Est Conv from MATLAB
+"""
+How to do the nuc Est Conv from MATLAB
Based on the code in MattSegCode/Matt Seg
GUI/@timelapseTraps/extractCellDataStacksParfor.m
-Especially lines 342 to 399.
+Especially lines 342 to 399.
This part only replicates the method to get the nuc_est_conv values
"""
import typing as t
diff --git a/src/extraction/core/functions/loaders.py b/src/extraction/core/functions/loaders.py
index ff83b20c..ce33f845 100644
--- a/src/extraction/core/functions/loaders.py
+++ b/src/extraction/core/functions/loaders.py
@@ -11,8 +11,8 @@ from extraction.core.functions.math_utils import div0
"""
Load functions for analysing cells and their background.
-Note that inspect.getmembers returns a list of function names and functions,
-and inspect.getfullargspec returns a function's arguments.
+Note that inspect.getmembers returns a list of function names and
+functions, and inspect.getfullargspec returns a function's arguments.
"""
--
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