Merge pull request #3 from vreuter/vr/pandas-table-like

Support pandas-like table with headers, and new `looptrace` (v0.5.0) output format

CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.2.0] - 2024-05-30
+
+### Changed
+* This project now can use `pandas` and parses a table-like file (CSV) _with_ header, to support upstream changes in data generation by `looptrace`.
+* Splitting old functionality out into separate modules
+
 ## [v0.1.0] - 2024-04-20
 
 ### Added

looptrace_loci_vis/__init__.py

@@ -1,3 +1,3 @@
 """Napari plugin for visualising locus-specific points from looptrace"""
 
-__version__ = "0.1.0"
+__version__ = "0.2.0"

looptrace_loci_vis/_const.py

@@ -0,0 +1,9 @@
+"""Plugin-wide constants"""
+
+from enum import Enum
+
+
+class PointColor(Enum):
+    # See: https://davidmathlogic.com/colorblind/
+    DEEP_SKY_BLUE = "#0C7BDC"
+    GOLDENROD = "#FFC20A"

looptrace_loci_vis/_types.py

@@ -0,0 +1,18 @@
+"""Type aliases used broadly"""
+
+from collections.abc import Callable
+from pathlib import Path
+from typing import Literal, Union
+
+from gertils.geometry import ZCoordinate
+from gertils.types import PixelArray
+
+CsvRow = list[str]
+FlatPointRecord = list[Union[float, ZCoordinate]]
+LayerParams = dict[str, object]
+ImageLayer = tuple[PixelArray, LayerParams, Literal["image"]]
+PointsLayer = tuple[list[FlatPointRecord], LayerParams, Literal["points"]]
+PathLike = str | Path
+PathOrPaths = PathLike | list[PathLike]
+QCFailReasons = str
+Reader = Callable[[PathLike], list[ImageLayer | PointsLayer]]

looptrace_loci_vis/point_record.py

@@ -0,0 +1,118 @@
+"""A single point's record in a file on disk."""
+
+import dataclasses
+from math import floor
+from typing import Union
+
+import numpy as np
+from gertils.geometry import ImagePoint3D, LocatableXY, LocatableZ, ZCoordinate
+from gertils.types import TimepointFrom0 as Timepoint
+from gertils.types import TraceIdFrom0 as TraceId
+from numpydoc_decorator import doc  # type: ignore[import-untyped]
+
+from ._types import FlatPointRecord
+
+
+@doc(
+    summary="",
+    parameters=dict(
+        trace_id="ID of the trace with which the locus spot is associated",
+        timepoint="Imaging timepoint in from which the point is coming",
+        point="Coordinates of the centroid of the Gaussian fit to the spot image pixel data",
+    ),
+)
+@dataclasses.dataclass(frozen=True, kw_only=True)
+class PointRecord(LocatableXY, LocatableZ):  # noqa: D101
+    trace_id: TraceId
+    timepoint: Timepoint
+    point: ImagePoint3D
+
+    def __post_init__(self) -> None:
+        bads: dict[str, object] = {}
+        if not isinstance(self.trace_id, TraceId):
+            bads["trace ID"] = self.trace_id  # type: ignore[unreachable]
+        if not isinstance(self.timepoint, Timepoint):
+            bads["timepoint"] = self.timepoint  # type: ignore[unreachable]
+        if not isinstance(self.point, ImagePoint3D):
+            bads["point"] = self.point  # type: ignore[unreachable]
+        if bads:
+            messages = "; ".join(f"Bad type ({type(v).__name__}) for {k}" for k, v in bads.items())
+            raise TypeError(f"Cannot create point record: {messages}")
+
+    @doc(summary="Flatten")
+    def flatten(self) -> FlatPointRecord:
+        """Create a simple list of components, as a row of layer data."""
+        return [
+            self.trace_id.get,
+            self.timepoint.get,
+            self.get_z_coordinate(),
+            self.get_y_coordinate(),
+            self.get_x_coordinate(),
+        ]
+
+    def get_x_coordinate(self) -> float:  # noqa: D102
+        return self.point.x
+
+    def get_y_coordinate(self) -> float:  # noqa: D102
+        return self.point.y
+
+    def get_z_coordinate(self) -> ZCoordinate:  # noqa: D102
+        return self.point.z
+
+    @doc(summary="Round point position to nearest z-slice")
+    def with_truncated_z(self) -> "PointRecord":  # noqa: D102
+        new_z: int = floor(self.get_z_coordinate())
+        result: PointRecord = self.with_new_z(new_z)
+        return result
+
+    @doc(
+        summary="Replace this instance's point with a copy with updated z.",
+        parameters=dict(z="New z-coordinate value"),
+    )
+    def with_new_z(self, z: int) -> "PointRecord":  # noqa: D102
+        pt = ImagePoint3D(x=self.point.x, y=self.point.y, z=z)
+        return dataclasses.replace(self, point=pt)
+
+
+@doc(
+    summary="Create ancillary points from main point",
+    parameters=dict(
+        r="The record to expand along z-axis",
+        z_max="The maximum z-coordinate",
+    ),
+    returns="""
+        List of layer data rows to represent the original point along
+        entire length of z-axis, paired with flag for each row
+        indicating whether it's true center or not
+    """,
+)
+def expand_along_z(  # noqa: D103
+    r: PointRecord, *, z_max: Union[float, np.float64]
+) -> tuple[list[PointRecord], list[bool]]:
+    if not isinstance(z_max, int | float | np.float64):
+        raise TypeError(f"Bad type for z_max: {type(z_max).__name__}")
+
+    r = r.with_truncated_z()
+    z_center = int(r.get_z_coordinate())
+    z_max = int(floor(z_max))
+    if not isinstance(z_center, int) or not isinstance(z_max, int):
+        raise TypeError(
+            f"Z center and Z max must be int; got {type(z_center).__name__} and"
+            f" {type(z_max).__name__}"
+        )
+
+    # Check that max z and center z make sense together.
+    if z_max < z_center:
+        raise ValueError(f"Max z must be at least as great as central z ({z_center})")
+
+    # Build the records and flags of where the center in z really is.
+    predecessors = [(r.with_new_z(i), False) for i in range(z_center)]
+    successors = [(r.with_new_z(i), False) for i in range(z_center + 1, z_max + 1)]
+    points, params = zip(*[*predecessors, (r, True), *successors], strict=False)
+
+    # Each record should give rise to a total of 1 + z_max records, since numbering from 0.
+    if len(points) != 1 + z_max:
+        raise RuntimeError(
+            f"Number of points generated from single spot center isn't as expected! Point={r}, z_max={z_max}, len(points)={len(points)}"
+        )
+    return points, params  # type: ignore[return-value]

looptrace_loci_vis/points_parser.py

@@ -0,0 +1,144 @@
+"""Abstractions related to points parsing"""
+
+import abc
+import csv
+from collections.abc import Iterable, Sized
+from enum import Enum
+from typing import Generic, Protocol, TypeVar
+
+import pandas as pd
+from gertils.geometry import ImagePoint3D
+from gertils.types import TimepointFrom0 as Timepoint
+from gertils.types import TraceIdFrom0 as TraceId
+
+from ._types import CsvRow, PathLike, QCFailReasons
+from .point_record import PointRecord
+
+Input = TypeVar("Input", contravariant=True)
+I1 = TypeVar("I1")
+I2 = TypeVar("I2", bound=Sized)
+
+
+class MappingLike(Protocol, Sized):  # noqa: D101
+    @abc.abstractmethod
+    def __getitem__(self, key: str) -> object: ...
+
+    @abc.abstractmethod
+    def __len__(self) -> int: ...
+
+
+class PointsParser(Protocol, Generic[Input]):
+    """Something capable of parsing a QC-pass or -fail CSV file"""
+
+    @classmethod
+    @abc.abstractmethod
+    def parse_all_qcpass(cls, data: Input) -> list[PointRecord]: ...  # noqa: D102
+
+    @classmethod
+    @abc.abstractmethod
+    def parse_all_qcfail(cls, data: Input) -> list[tuple[PointRecord, QCFailReasons]]: ...  # noqa: D102
+
+
+class IterativePointsParser(Generic[I1, I2], PointsParser[I1]):
+    """Something that yields records, each of type I2 from value of type I1, to parse QC-pass/-fail points"""
+
+    @classmethod
+    @abc.abstractmethod
+    def _gen_records(cls, data: I1) -> Iterable[I2]: ...
+
+    @classmethod
+    @abc.abstractmethod
+    def _parse_single_qcpass_record(cls, record: I2) -> PointRecord: ...
+
+    @classmethod
+    @abc.abstractmethod
+    def _parse_single_qcfail_record(cls, record: I2) -> tuple[PointRecord, QCFailReasons]: ...
+
+    @classmethod
+    def parse_all_qcpass(cls, data: I1) -> list[PointRecord]:  # noqa: D102
+        return [cls._parse_single_qcpass_record(r) for r in cls._gen_records(data)]
+
+    @classmethod
+    def parse_all_qcfail(cls, data: I1) -> list[tuple[PointRecord, QCFailReasons]]:  # noqa: D102
+        return [cls._parse_single_qcfail_record(r) for r in cls._gen_records(data)]
+
+
+class HeadedTraceTimePointParser(IterativePointsParser[PathLike, MappingLike]):
+    """Something capable of parsing a headed CSV of QC-pass/-fail points records"""
+
+    TIME_INDEX_COLUMN = "timeIndex"
+
+    @classmethod
+    def _gen_records(cls, data: PathLike) -> Iterable[MappingLike]:
+        for _, row in pd.read_csv(data).iterrows():
+            yield row
+
+    @classmethod
+    def _parse_single_qcpass_record(cls, record: MappingLike) -> PointRecord:
+        trace = TraceId(int(record["traceIndex"]))  # type: ignore[call-overload]
+        timepoint = Timepoint(int(record[cls.TIME_INDEX_COLUMN]))  # type: ignore[call-overload]
+        z = float(record["z"])  # type: ignore[arg-type]
+        y = float(record["y"])  # type: ignore[arg-type]
+        x = float(record["x"])  # type: ignore[arg-type]
+        point = ImagePoint3D(z=z, y=y, x=x)
+        return PointRecord(trace_id=trace, timepoint=timepoint, point=point)
+
+    @classmethod
+    def _parse_single_qcfail_record(cls, record: MappingLike) -> tuple[PointRecord, QCFailReasons]:
+        """A fail record parses the same as a pass one, just with one additional field for QC fail reasons."""
+        pt_rec = cls._parse_single_qcpass_record(record)
+        fail_code = record["failCode"]
+        if not isinstance(fail_code, str):
+            raise TypeError(f"failCode is not str, but {type(fail_code).__name__}")
+        fail_code: str = str(fail_code)  # type: ignore[no-redef]
+        return pt_rec, fail_code
+
+
+class HeadlessTraceTimePointParser(IterativePointsParser[PathLike, CsvRow]):
+    """Parser for input file with no header, and field for trace ID and timepoint in addition to coordinates"""
+
+    class InputFileColumn(Enum):
+        """Indices of the different columns to parse as particular fields"""
+
+        TRACE = 0
+        TIMEPOINT = 1
+        Z = 2
+        Y = 3
+        X = 4
+        QC = 5
+
+        @property
+        def get(self) -> int:
+            """Alias for the value of this enum member"""
+            return self.value
+
+    _number_of_columns = sum(1 for _ in InputFileColumn)
+
+    @classmethod
+    def _parse_single_record(cls, r: CsvRow, *, exp_len: int) -> PointRecord:
+        if not isinstance(r, list):
+            raise TypeError(f"Record to parse must be list, not {type(r).__name__}")
+        if len(r) != exp_len:
+            raise ValueError(f"Expected record of length {exp_len} but got {len(r)}: {r}")
+        trace = TraceId(int(r[cls.InputFileColumn.TRACE.get]))
+        timepoint = Timepoint(int(r[cls.InputFileColumn.TIMEPOINT.get]))
+        z = float(r[cls.InputFileColumn.Z.get])
+        y = float(r[cls.InputFileColumn.Y.get])
+        x = float(r[cls.InputFileColumn.X.get])
+        point = ImagePoint3D(z=z, y=y, x=x)
+        return PointRecord(trace_id=trace, timepoint=timepoint, point=point)
+
+    @classmethod
+    def _gen_records(cls, data: PathLike) -> Iterable[CsvRow]:
+        with open(data, newline="") as fh:  # noqa: PTH123
+            return list(csv.reader(fh))
+
+    @classmethod
+    def _parse_single_qcpass_record(cls, record: CsvRow) -> PointRecord:
+        return cls._parse_single_record(record, exp_len=cls._number_of_columns - 1)
+
+    @classmethod
+    def _parse_single_qcfail_record(cls, record: CsvRow) -> tuple[PointRecord, QCFailReasons]:
+        pt_rec = cls._parse_single_record(record, exp_len=cls._number_of_columns)
+        fail_code = record[cls.InputFileColumn.QC.get]
+        return pt_rec, fail_code