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Merged
Czaki merged 2 commits into from
Jul 9, 2025
Merged

feat: Add measurement of distance form nucleus center and border #8

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496eb08
add measurement of distance form nucleus center and border
Czaki Jul 8, 2025
46a5b75
Merge remote-tracking branch 'origin/main' into distance_measure
Czaki Jul 9, 2025
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8 changes: 8 additions & 0 deletions src/PartSeg_smfish/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,14 @@ def register():
RegisterEnum.roi_mask_segmentation_algorithm,
)
register_fun(measurement.ComponentType, RegisterEnum.analysis_measurement)
register_fun(
measurement.DistanceToNucleusCenter,
RegisterEnum.analysis_measurement,
)
register_fun(
measurement.DistanceFromNucleusBorder,
RegisterEnum.analysis_measurement,
)

if getattr(sys, "frozen", False):
from napari.plugins import plugin_manager
Expand Down
112 changes: 112 additions & 0 deletions src/PartSeg_smfish/measurement.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,13 @@
import numpy as np
from PartSegCore import autofit as af
from PartSegCore.analysis.measurement_base import (
AreaType,
Leaf,
MeasurementMethodBase,
PerComponent,
)
from PartSegCore.analysis.measurement_calculation import get_border
from sympy import symbols


class ComponentType(MeasurementMethodBase):
Expand All @@ -28,3 +32,111 @@ def calculate_property(roi_annotation, _component_num, **kwargs):
@classmethod
def get_units(cls, ndim):
return 1


class DistanceToNucleusCenter(MeasurementMethodBase):
text_info = (
"Distance to nucleus center",
"Distance to nucleus center in units",
)

@classmethod
def get_fields(cls):
return []

@classmethod
def need_full_data(cls):
return True

@classmethod
def get_starting_leaf(cls):
return Leaf(
name=cls.text_info[0],
area=AreaType.ROI,
per_component=PerComponent.Yes,
)

@staticmethod
def calculate_property(
area_array,
roi_alternative: dict[str, np.ndarray],
help_dict: dict,
result_scalar: float,
voxel_size: tuple[float, float, float],
**kwargs,
):
if "nucleus_center" not in help_dict:
nucleus = roi_alternative["nucleus"]
help_dict["nucleus_center"] = (
af.density_mass_center(nucleus, voxel_size) * result_scalar
)
nucleus_center = help_dict["nucleus_center"]
roi_center = (
af.density_mass_center(area_array, voxel_size) * result_scalar
)
return np.sqrt(np.sum((nucleus_center - roi_center) ** 2))

@classmethod
def get_units(cls, ndim):
return symbols("{}")

Comment on lines +37 to +82
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@coderabbitai coderabbitai bot Jul 9, 2025 •
edited
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🛠️ Refactor suggestion

Fix the units method to return proper units.

The DistanceToNucleusCenter class implementation is correct for calculating Euclidean distance with good caching optimization. However, the get_units method returns an empty symbolic unit which likely isn't intended.

 @classmethod
 def get_units(cls, ndim):
-    return symbols("{}")
+    return symbols("μm")  # or appropriate unit symbol

The distance calculation logic is sound - it computes the Euclidean distance between the density mass centers of the ROI and nucleus, with proper scaling by result_scalar.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
class DistanceToNucleusCenter(MeasurementMethodBase):
text_info = (
"Distance to nucleus center",
"Distance to nucleus center in units",
)
@classmethod
def get_fields(cls):
return []
@classmethod
def need_full_data(cls):
return True
@classmethod
def get_starting_leaf(cls):
return Leaf(
name=cls.text_info[0],
area=AreaType.ROI,
per_component=PerComponent.Yes,
)
@staticmethod
def calculate_property(
area_array,
roi_alternative: dict[str, np.ndarray],
help_dict: dict,
result_scalar: float,
voxel_size: tuple[float, float, float],
**kwargs,
):
if "nucleus_center" not in help_dict:
nucleus = roi_alternative["nucleus"]
help_dict["nucleus_center"] = (
af.density_mass_center(nucleus, voxel_size) * result_scalar
)
nucleus_center = help_dict["nucleus_center"]
roi_center = (
af.density_mass_center(area_array, voxel_size) * result_scalar
)
return np.sqrt(np.sum((nucleus_center - roi_center) ** 2))
@classmethod
def get_units(cls, ndim):
return symbols("{}")
@classmethod
def get_units(cls, ndim):
- return symbols("{}")
+ return symbols("μm") # or appropriate unit symbol
🤖 Prompt for AI Agents 
In src/PartSeg_smfish/measurement.py between lines 37 and 82, the get_units
method in the DistanceToNucleusCenter class currently returns an empty symbolic
unit which is incorrect. Update this method to return the appropriate unit for
distance measurement, such as a length unit symbol, to correctly represent the
units of the calculated distance.

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@Czaki Czaki Jul 9, 2025

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The unit is determined by result_scalar and the proper text value is set using str.format when printing reesult.

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@coderabbitai coderabbitai bot Jul 9, 2025

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@Czaki Thank you for the clarification! You're absolutely right - I misunderstood how the unit system works in this codebase. The symbols("{}") creates a placeholder that gets filled in later using str.format when the results are printed, with the actual unit determined by the result_scalar. This is a much more flexible approach than hardcoding the unit symbol.

I appreciate you taking the time to explain this implementation detail!

✏️ Learnings added 
Learnt from: Czaki
PR: 4DNucleome/PartSeg-smfish#8
File: src/PartSeg_smfish/measurement.py:37-82
Timestamp: 2025-07-09T23:03:57.430Z
Learning: In PartSeg measurement classes, the `get_units()` method returns `symbols("{}")` as a placeholder that gets filled in later using `str.format` when printing results. The actual unit is determined by the `result_scalar` parameter, making the unit system dynamic and flexible.

Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.


class DistanceFromNucleusBorder(MeasurementMethodBase):
text_info = (
"Distance from nucleus border",
"Distance from nucleus border in units",
)

@classmethod
def get_fields(cls):
return []

@classmethod
def need_full_data(cls):
return True

@classmethod
def get_starting_leaf(cls):
return Leaf(
name=cls.text_info[0],
area=AreaType.ROI,
per_component=PerComponent.Yes,
)

@staticmethod
def calculate_property(
area_array,
roi_alternative: dict[str, np.ndarray],
help_dict: dict,
result_scalar: float,
roi_annotation: dict,
_component_num: int,
voxel_size: tuple[float, float, float],
**kwargs,
):
if "nucleus_border" not in help_dict:
nucleus = roi_alternative["nucleus"]
area_pos = np.transpose(np.nonzero(get_border(nucleus))).astype(
float
)
area_pos += 0.5
for i, val in enumerate(
(x * result_scalar for x in reversed(voxel_size)), start=1
):
area_pos[:, -i] *= val
help_dict["nucleus_border"] = area_pos

nucleus_border = help_dict["nucleus_border"]
roi_center = (
af.density_mass_center(area_array, voxel_size) * result_scalar
)
res = np.sqrt(
np.min(np.sum((nucleus_border - roi_center) ** 2, axis=1))
)
if roi_annotation[_component_num].get("type") == "Nucleus":
return -res
return res

@classmethod
def get_units(cls, ndim):
return symbols("{}")
Comment on lines +84 to +142
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💡 Verification agent

🧩 Analysis chain

Fix the units method and verify coordinate scaling logic.

The DistanceFromNucleusBorder class implements a complex but correct distance calculation. The coordinate scaling logic appears sound, but the units issue needs fixing.

 @classmethod
 def get_units(cls, ndim):
-    return symbols("{}")
+    return symbols("μm")  # or appropriate unit symbol

The implementation correctly:

  • Caches nucleus border coordinates for efficiency
  • Scales coordinates by voxel size and result_scalar
  • Finds minimum distance to border points
  • Returns negative distance for "Nucleus" ROI type (indicating inside the nucleus)

Please verify that the coordinate scaling logic in lines 123-126 correctly handles the dimensionality and ordering:

🏁 Script executed:

#!/bin/bash
# Verify the coordinate scaling logic matches the expected dimensionality
ast-grep --pattern 'for i, val in enumerate($$$):
    area_pos[:, -i] *= val'

Length of output: 397

🏁 Script executed:

#!/bin/bash
head -n 40 src/PartSeg_smfish/measurement.py

Length of output: 1062

🏁 Script executed:

#!/bin/bash
rg -n "def get_units" src/PartSeg_smfish/measurement.py -B3 -A3

Length of output: 500

Fix the units for DistanceFromNucleusBorder

The coordinate-scaling loop (Lines 123–126) correctly applies voxel_size and result_scalar to each axis in reverse order. Only the get_units method needs updating to reflect a physical length unit.

File: src/PartSeg_smfish/measurement.py

@@ class DistanceFromNucleusBorder(MeasurementMethodBase):
 @classmethod
 def get_units(cls, ndim):
-    return symbols("{}")
+    # Return the physical length unit, e.g., micrometers
+    return symbols("µm")
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
class DistanceFromNucleusBorder(MeasurementMethodBase):
text_info = (
"Distance from nucleus border",
"Distance from nucleus border in units",
)
@classmethod
def get_fields(cls):
return []
@classmethod
def need_full_data(cls):
return True
@classmethod
def get_starting_leaf(cls):
return Leaf(
name=cls.text_info[0],
area=AreaType.ROI,
per_component=PerComponent.Yes,
)
@staticmethod
def calculate_property(
area_array,
roi_alternative: dict[str, np.ndarray],
help_dict: dict,
result_scalar: float,
roi_annotation: dict,
_component_num: int,
voxel_size: tuple[float, float, float],
**kwargs,
):
if "nucleus_border" not in help_dict:
nucleus = roi_alternative["nucleus"]
area_pos = np.transpose(np.nonzero(get_border(nucleus))).astype(
float
)
area_pos += 0.5
for i, val in enumerate(
(x * result_scalar for x in reversed(voxel_size)), start=1
):
area_pos[:, -i] *= val
help_dict["nucleus_border"] = area_pos
nucleus_border = help_dict["nucleus_border"]
roi_center = (
af.density_mass_center(area_array, voxel_size) * result_scalar
)
res = np.sqrt(
np.min(np.sum((nucleus_border - roi_center) ** 2, axis=1))
)
if roi_annotation[_component_num].get("type") == "Nucleus":
return -res
return res
@classmethod
def get_units(cls, ndim):
return symbols("{}")
@classmethod
def get_units(cls, ndim):
- return symbols("{}")
+ # Return the physical length unit, e.g., micrometers
+ return symbols("µm")
🤖 Prompt for AI Agents 
In src/PartSeg_smfish/measurement.py around lines 84 to 142, the get_units
method currently returns an empty symbol string, which does not reflect the
physical length units used in the distance calculation. Update the get_units
method to return the appropriate physical length unit symbol, such as "µm" or
"um", to correctly represent the units of the distance from the nucleus border.