Merge pull request #5 from fmi-faim/single-plane

Switch to lark for parsing nd file contents

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3

pyproject.toml

@@ -7,7 +7,7 @@ name = "metamorph-mda-parser"
 dynamic = ["version"]
 description = 'Light-weight parsing of Metamorph/VisiView .nd files.'
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = "BSD-3-Clause"
 keywords = []
 authors = [
@@ -16,16 +16,16 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
+  "lark",
   "pandas",
+  "pydantic",
 ]
 
 [project.urls]
@@ -54,7 +54,7 @@ cov = [
 ]
 
 [[tool.hatch.envs.all.matrix]]
-python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
+python = ["3.10", "3.11", "3.12"]
 
 [tool.hatch.envs.types]
 dependencies = [
@@ -76,8 +76,12 @@ metamorph_mda_parser = ["src/metamorph_mda_parser", "*/metamorph-mda-parser/src/
 tests = ["tests", "*/metamorph-mda-parser/tests"]
 
 [tool.coverage.report]
+show_missing = true
 exclude_lines = [
   "no cov",
   "if __name__ == .__main__.:",
   "if TYPE_CHECKING:",
 ]
+
+[tool.ruff.lint.flake8-type-checking]
+runtime-evaluated-base-classes = ["pydantic.BaseModel"]

src/metamorph_mda_parser/lark.py

@@ -0,0 +1,36 @@
+from lark import Lark, Transformer
+
+
+class NDInfoTransformer(Transformer):
+    def __init__(self):
+        self.wave_names = []
+        self.wave_do_z = []
+        self.stage_positions = []
+
+    def start(self, items):
+        result = dict(i for i in items if i is not None)
+        result["WaveNames"] = self.wave_names
+        result["WaveDoZ"] = self.wave_do_z
+        result["StagePositions"] = self.stage_positions
+        return result
+
+    def line(self, key_value):
+        key, value = key_value
+        if key.startswith("WaveName"):
+            self.wave_names.append(value)
+            return None  # We handle WaveName entries separately
+        if key.startswith("Stage"):
+            self.stage_positions.append(value)
+            return None  # We handle Stage entries separately
+        if key.startswith("WaveDoZ"):
+            self.wave_do_z.append(value)
+            return None  # We handle WaveDoZ entries separately
+        return (key, value)
+
+    def boolean_value(self, b):
+        return b[0].value == "TRUE"
+
+
+def parse(content):
+    parser = Lark.open("nd_grammar.lark", rel_to=__file__, parser="lalr", transformer=NDInfoTransformer())
+    return parser.parse(content)

src/metamorph_mda_parser/nd.py

@@ -1,89 +1,48 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Callable, Literal
-
-if TYPE_CHECKING:
-    from pathlib import Path
+from pathlib import Path
+from typing import Literal
 
 import pandas as pd
+from pydantic import AliasGenerator, BaseModel, ConfigDict
+from pydantic.alias_generators import to_pascal
+
+from metamorph_mda_parser.lark import parse
 
 
-class NdInfo:
+class NdInfo(BaseModel):
+    model_config = ConfigDict(
+        alias_generator=AliasGenerator(
+            validation_alias=to_pascal,
+        ),
+    )
+
     path: Path
     name: str
     version: Literal["1.0", "2.0"]
     description: str
     do_timelapse: bool
     do_stage: bool
     do_wave: bool
-    do_z: bool
-    stage_positions: list[str]
-    wave_names: list[str]
-    wave_do_z: list[bool]
-    n_timepoints: int
-    n_z_steps: int
-    z_step_size: float
+    do_z_series: bool
+    stage_positions: list[str] = []
+    wave_names: list[str] = []
+    wave_do_z: list[bool] = []
+    n_stage_positions: int = 1
+    n_time_points: int = 1
+    n_z_steps: int = 1
+    z_step_size: float | None = None
     wave_in_file_name: bool
 
-    def __init__(self, path: Path):
-        self.path = path
-        self.name = path.stem
-        self._parse_nd()
-
-    def _parse_nd(self) -> None:
-        with open(self.path) as nd:
-            # Version
-            self.version = self._parse_line(nd.readline(), "NDInfoFile", self._extract_version)
-            self.description = self._parse_line(nd.readline(), "Description", str)
-            self.start_time = self._parse_line(nd.readline(), "StartTime1", str)
-            # Time lapse
-            self.do_timelapse = self._parse_line(nd.readline(), "DoTimelapse", self._parse_bool)
-            if self.do_timelapse:
-                self.n_timepoints = self._parse_line(nd.readline(), "NTimePoints", int)
-
-            # Stage positions
-            self.do_stage = self._parse_line(nd.readline(), "DoStage", self._parse_bool)
-            if self.do_stage:
-                n_stage_positions = self._parse_line(nd.readline(), "NStagePositions", int)
-                self.stage_positions = []
-                for s in range(n_stage_positions):
-                    self.stage_positions.append(self._parse_line(nd.readline(), f"Stage{s+1}", str))
-
-            # Wavelengths
-            self.do_wave = self._parse_line(nd.readline(), "DoWave", self._parse_bool)
-            if self.do_wave:
-                n_wavelengths = self._parse_line(nd.readline(), "NWavelengths", int)
-                self.wave_names = []
-                self.wave_do_z = []
-                for w in range(n_wavelengths):
-                    self.wave_names.append(self._parse_line(nd.readline(), f"WaveName{w+1}", str))
-                    self.wave_do_z.append(self._parse_line(nd.readline(), f"WaveDoZ{w+1}", self._parse_bool))
-
-            # Z steps
-            self.do_z = self._parse_line(nd.readline(), "DoZSeries", self._parse_bool)
-            self.n_z_steps = self._parse_line(nd.readline(), "NZSteps", int)
-            self.z_step_size = self._parse_line(nd.readline(), "ZStepSize", float)
-
-            self.wave_in_file_name = self._parse_line(nd.readline(), "WaveInFileName", self._parse_bool)
-
-            # End of file
-            last_line = nd.readline()
-            if last_line.strip(' "\n') != "EndFile":
-                message = f"Expected end of file, got: {last_line}"
-                raise ValueError(message)
-
-    def _parse_line(self, line: str, key: str, value_function: Callable):
-        tokens = line.split(",")
-        if tokens[0].strip(' "') != key:
-            message = f"Invalid nd file contents.\n\texpected: {key}\n\tgot: {line}"
-            raise ValueError(message)
-        return value_function(tokens[1].strip(' "\n'))
-
-    def _extract_version(self, value: str) -> str:
-        return value[8:]
-
-    def _parse_bool(self, value: str) -> bool:
-        return value.lower() == "true"
+    @staticmethod
+    def from_path(path: Path):
+        with open(path) as f:
+            content = f.read()
+        result = parse(content)
+        result["Path"] = path
+        result["Name"] = path.stem
+        result["Version"] = "1.0"  # HACK
+        return NdInfo(**result)
 
     def _wavelengths(self):
         for i, w in enumerate(self.wave_names):
@@ -92,7 +51,7 @@ def _wavelengths(self):
                     i,
                     w,
                     f"_w{i+1}{w}" if self.wave_in_file_name else "",
-                    self.wave_do_z[i],
+                    self.wave_do_z[i] if self.wave_do_z else False,
                 )
 
     def _stage_positions(self):
@@ -102,7 +61,7 @@ def _stage_positions(self):
 
     def _timepoints(self):
         if self.do_timelapse:
-            for t in range(self.n_timepoints):
+            for t in range(self.n_time_points):
                 yield t, f"_t{t+1}"
 
     def _get_path_channel_position_time(self):

src/metamorph_mda_parser/nd_grammar.lark

@@ -0,0 +1,40 @@
+start: line+ "\"EndFile\""
+line: _QUOTE _special_key _QUOTE "," _special_value
+    | _QUOTE _string_key _QUOTE "," _QUOTE _string_value _QUOTE
+    | _QUOTE _boolean_key _QUOTE "," boolean_value
+    | _QUOTE _integer_key _QUOTE "," _integer_value
+    | _QUOTE _float_key _QUOTE "," _float_value
+
+_special_key: /NDInfoFile/
+            | /Description/
+            | /StartTime[0-9]+/
+_special_value: /.+/
+
+_string_key: /WaveName[0-9]+/
+           | /Stage[0-9]+/
+_string_value: /[^"]+/
+
+_boolean_key: /DoTimelapse/
+            | /DoStage/
+            | /DoWave/
+            | /DoZSeries/
+            | /WaveInFileName/
+            | /WaveDoZ[0-9]+/
+boolean_value: BOOLEAN
+
+_integer_key: /NWavelengths/
+            | /NStagePositions/
+            | /NTimePoints/
+            | /NZSteps/
+_integer_value: INT
+
+_float_key: /ZStepSize/
+_float_value: DECIMAL | INT
+
+%import common.INT
+%import common.DECIMAL
+%import common.WS
+%ignore WS
+
+BOOLEAN: "TRUE" | "FALSE"
+_QUOTE: "\""

tests/resources/sample_4ch_1pos_1z.nd

@@ -0,0 +1,14 @@
+"NDInfoFile", Version 1.0
+"Description", File recreated from images.
+"StartTime1", 20240603 12:25:48.610
+"DoTimelapse", FALSE
+"DoStage", FALSE
+"DoWave", TRUE
+"NWavelengths", 4
+"WaveName1", "confDAPI"
+"WaveName2", "confGFP"
+"WaveName3", "confmCherry"
+"WaveName4", "confCy5"
+"DoZSeries", FALSE
+"WaveInFileName", TRUE
+"EndFile"

tests/test_nd.py

@@ -15,8 +15,13 @@ def sample_2ch_75pos_361t():
     return Path("tests/resources/sample_2ch_75pos_361t.nd")
 
 
+@pytest.fixture
+def sample_4ch_1pos_1z():
+    return Path("tests/resources/sample_4ch_1pos_1z.nd")
+
+
 def test_sample_4ch_4pos(sample_4ch_4pos):
-    nd_info = NdInfo(sample_4ch_4pos)
+    nd_info = NdInfo.from_path(sample_4ch_4pos)
 
     assert nd_info.version == "1.0"
     assert nd_info.description == "File recreated from images."
@@ -25,7 +30,7 @@ def test_sample_4ch_4pos(sample_4ch_4pos):
     assert len(nd_info.stage_positions) == 4
     assert nd_info.do_wave
     assert len(nd_info.wave_names) == 4
-    assert nd_info.do_z
+    assert nd_info.do_z_series
     assert nd_info.n_z_steps == 42
     assert nd_info.z_step_size == 3.0
     assert nd_info.wave_in_file_name
@@ -47,17 +52,17 @@ def test_sample_4ch_4pos(sample_4ch_4pos):
 
 
 def test_sample_2ch_75pos_361t(sample_2ch_75pos_361t):
-    nd_info = NdInfo(sample_2ch_75pos_361t)
+    nd_info = NdInfo.from_path(sample_2ch_75pos_361t)
 
     assert nd_info.version == "1.0"
     assert nd_info.description == "File recreated from images."
     assert nd_info.do_timelapse
-    assert nd_info.n_timepoints == 361
+    assert nd_info.n_time_points == 361
     assert nd_info.do_stage
     assert len(nd_info.stage_positions) == 75
     assert nd_info.do_wave
     assert len(nd_info.wave_names) == 2
-    assert nd_info.do_z
+    assert nd_info.do_z_series
     assert nd_info.n_z_steps == 25
     assert nd_info.z_step_size == 2.0
     assert nd_info.wave_in_file_name
@@ -66,3 +71,26 @@ def test_sample_2ch_75pos_361t(sample_2ch_75pos_361t):
     files = nd_info.get_files()
 
     assert len(files) == 54150
+
+
+def test_sample_4ch_1pos_1z(sample_4ch_1pos_1z):
+    nd_info = NdInfo.from_path(sample_4ch_1pos_1z)
+
+    assert nd_info.version == "1.0"
+    assert nd_info.description == "File recreated from images."
+    assert not nd_info.do_timelapse
+    assert nd_info.n_time_points == 1
+    assert not nd_info.do_stage
+    assert len(nd_info.stage_positions) == 0
+    assert nd_info.do_wave
+    assert len(nd_info.wave_names) == 4
+    assert not nd_info.do_z_series
+    assert nd_info.n_z_steps == 1
+    assert nd_info.z_step_size is None
+    assert nd_info.wave_in_file_name
+    assert nd_info.wave_names == ["confDAPI", "confGFP", "confmCherry", "confCy5"]
+
+    files = nd_info.get_files()
+
+    assert len(files) == 4
+    assert all(p.suffix == ".tif" for p in files["path"])