From 82c3183a340f39b136a8e54dcd7b49231da5aa28 Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Wed, 22 Jan 2025 17:15:08 -0500 Subject: [PATCH 1/5] fix tilejson --- .../tabular-to-microjson-tool/pyproject.toml | 5 +- .../tabular_to_microjson/__main__.py | 30 +- .../tabular_to_microjson/microjson_overlay.py | 342 +++++++----------- .../tabular_to_microjson/utils.py | 208 +++++++++++ 4 files changed, 359 insertions(+), 226 deletions(-) create mode 100644 visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py diff --git a/visualization/tabular-to-microjson-tool/pyproject.toml b/visualization/tabular-to-microjson-tool/pyproject.toml index 81200d67a..1ef592ff8 100644 --- a/visualization/tabular-to-microjson-tool/pyproject.toml +++ b/visualization/tabular-to-microjson-tool/pyproject.toml @@ -7,13 +7,12 @@ readme = "README.md" packages = [{include = "polus", from = "src"}] [tool.poetry.dependencies] -python = ">=3.9,<4.0" +python = "<3.12,>=3.9.15" typer = "^0.7.0" filepattern = "^2.0.1" tqdm = "^4.65.0" pandas = "^2.0.3" -microjson = "^0.1.9" -vaex = "^4.17.0" +microjson = "^0.4.1" pydantic = "^2.4.2" pyarrow = ">=16.0,<17.0" diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py index 9aced4ee6..d90f79e24 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py @@ -59,6 +59,11 @@ def main( # noqa: PLR0913 "--geometryType", help="Type of Geometry", ), + tile_json: Optional[bool] = typer.Option( + False, + "--tileJson", + help="Tile JSON layer", + ), out_dir: pathlib.Path = typer.Option( ..., "--outDir", @@ -77,6 +82,7 @@ def main( # noqa: PLR0913 logger.info(f"geometryType = {geometry_type}") logger.info(f"stitchPattern = {stitch_pattern}") logger.info(f"groupBy = {group_by}") + logger.info(f"tile_json = {tile_json}") logger.info(f"outDir = {out_dir}") inp_dir = inp_dir.resolve() @@ -86,27 +92,19 @@ def main( # noqa: PLR0913 files = [file[1][0] for file in fps()] + stitch_path = [ + st for st in stitch_dir.iterdir() if st.suffix == ".txt" and st.is_file() + ][0] + with ThreadPoolExecutor(max_workers=num_workers) as executor: for file in tqdm(files, desc="Creating overlays", total=len(files)): - fname = pathlib.Path(file).stem - stitch_path = stitch_dir.joinpath(f"{fname}.txt") - if geometry_type == "Polygon": - poly = mo.PolygonSpec( - stitch_path=str(stitch_path), - stitch_pattern=stitch_pattern, - group_by=group_by, - ) - else: - poly = mo.PointSpec( - stitch_path=str(stitch_path), - stitch_pattern=stitch_pattern, - group_by=group_by, - ) - micro_model = mo.RenderOverlayModel( file_path=file, - coordinates=poly.get_coordinates, geometry_type=geometry_type, + stitch_path=stitch_path, + stitch_pattern=stitch_pattern, + group_by=group_by, + tile_json=tile_json, out_dir=out_dir, ) executor.submit(micro_model.microjson_overlay) diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py index 6e249c1d3..583a94c5f 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py @@ -5,15 +5,16 @@ from pathlib import Path from typing import Any from typing import Optional -from typing import Union import filepattern as fp import microjson.model as mj import numpy as np -import pydantic -import vaex -from pydantic import root_validator -from pydantic import validator +import polus.images.visualization.tabular_to_microjson.utils as ut +import pyarrow as pa +import pyarrow.csv as pcsv +import pyarrow.feather as pa_feather +from pydantic import Field +from pydantic import field_validator logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) @@ -22,75 +23,7 @@ EXT = (".arrow", ".feather") -def convert_vaex_dataframe(file_path: Path) -> vaex.dataframe.DataFrame: - """The vaex reading of tabular data with (".csv", ".feather", ".arrow") format. - - Args: - file_path: Path to tabular data. - - Returns: - A vaex dataframe. - """ - if file_path.name.endswith(".csv"): - return vaex.read_csv(Path(file_path), convert=True, chunk_size=5_000_000) - if file_path.name.endswith(EXT): - return vaex.open(Path(file_path)) - return None - - -class CustomOverlayModel(pydantic.BaseModel): - """Setting up configuration for pydantic base model.""" - - class Config: - """Model configuration.""" - - extra = "allow" - allow_population_by_field_name = True - - -class Validator(CustomOverlayModel): - """Validate stiching vector path and stiching pattern fields. - - This validates values passed for stitch_path and stitch_pattern attributes. - - Args: - stitch_path: Path to the stitching vector, containing x and y image positions. - stitch_pattern: Pattern to parse image filenames in stitching vector. - - Returns: - Attribute values - - """ - - stitch_path: str - stitch_pattern: str - - @root_validator(pre=True) - def validate_stitch_path(cls, values: dict) -> dict: # noqa: N805 - """Validate stitch path and stitch pattern.""" - stitch_path = values.get("stitch_path") - stitch_pattern = values.get("stitch_pattern") - if stitch_path is not None and not Path(stitch_path).exists(): - msg = "Stitching path does not exists!! Please do check path again" - raise ValueError(msg) - if stitch_path is not None and Path(stitch_path).exists(): - with Path.open(Path(stitch_path)) as f: - line = f.readlines() - if line is None: - msg = ( - "Stitching vector is empty so grid positions cannot be defined" - ) - raise ValueError(msg) - if stitch_path is not None and Path(stitch_path).exists(): - files = fp.FilePattern(stitch_path, stitch_pattern) - if len(files) == 0: - msg = "Define stitch pattern again!!! as it is unable to parse file" - raise ValueError(msg) - - return values - - -class PolygonSpec(Validator): +class PolygonSpec(ut.StitchingValidator): """Polygon is a two-dimensional planar shape with straight sides. This generates rectangular polygon coordinates from (x, y) coordinate positions. @@ -105,11 +38,8 @@ class PolygonSpec(Validator): """ - stitch_path: str - stitch_pattern: str group_by: Optional[str] = None - @property def get_coordinates(self) -> list[Any]: """Generate rectangular polygon coordinates.""" files = fp.FilePattern(self.stitch_path, self.stitch_pattern) @@ -158,10 +88,12 @@ def get_coordinates(self) -> list[Any]: return mapped_coordinates -class PointSpec(Validator): - """Polygon is a two-dimensional planar shape with straight sides. +class PointSpec(ut.StitchingValidator): + """Generate mapped coordinates for rectangular polygons based on image positions. - This generates rectangular polygon coordinates from (x, y) coordinate positions. + This class calculates the centroid positions of rectangular polygons derived from + (x, y) coordinate positions in a stitching vector. It supports optional grouping + of filenames for structured output. Args: stitch_path: Path to the stitching vector, containing x and y image positions. @@ -169,21 +101,22 @@ class PointSpec(Validator): group_by: Variable to group image filenames in stitching vector. Returns: - A list of tuples of centroids of a rectangular polygon.. + A list of dictionaries, each containing: + - "file": The parsed filename. + - "coordinates": A tuple representing the centroid of the calculated rectangle. """ - stitch_path: str + stitch_path: Path stitch_pattern: str group_by: Optional[str] = None - @property def get_coordinates(self) -> list[Any]: """Generate rectangular polygon coordinates.""" files = fp.FilePattern(self.stitch_path, self.stitch_pattern) - self.group_by = None if self.group_by == "None" else self.group_by + self.group_by = None if self.group_by in {None, "None"} else self.group_by - if self.group_by is not None: + if self.group_by: var_list = files.get_unique_values() var_dict = {k: len(v) for k, v in var_list.items() if k == self.group_by} gp_value = var_dict[self.group_by] @@ -225,90 +158,110 @@ def get_coordinates(self) -> list[Any]: return mapped_coordinates -class ValidatedProperties(mj.Properties): - """Properties with validation.""" - - @validator("string", pre=True, each_item=True) - def validate_str( - cls, - v: Union[str, None], - ) -> str: # noqa: N805 - """Validate string.""" - if v is None: - return "" - return v - - @validator("numeric", pre=True, each_item=True) - def validate_num( - cls, - v: Union[int, None], - ) -> Union[int, None]: # noqa: N805 - """Validate numeric.""" - if v is None: - return np.nan - return v - - -class RenderOverlayModel(CustomOverlayModel): +class RenderOverlayModel(ut.StitchingValidator): """Generate JSON overlays using microjson python package. Args: file_path: Path to input file. - coordinates: List of geometry coordinates. - geometry_type: Type of geometry (Polygon, Points, bbbox). + geometry_type: Type of geometry (Polygon, Points). + stitch_path: Path to the stitching vector, containing x and y image positions. + stitch_pattern: Pattern to parse image filenames in stitching vector. + group_by: Variable to group image filenames in stitching vector. + tile_json: Convert microjson to tile json pyramid. out_dir: Path to output directory. """ - file_path: Path - coordinates: list[Any] - geometry_type: str + file_path: Path = Field(..., description="Input file path.") + geometry_type: str = Field( + ..., description="Type of geometry: 'polygon' or 'point'", + ) + stitch_path: Path + stitch_pattern: str + group_by: Optional[str] = None + tile_json: Optional[bool] = False out_dir: Path - @pydantic.validator("file_path", pre=True) + @field_validator("file_path") def validate_file_path(cls, value: Path) -> Path: # noqa: N805 - """Validate file path.""" + """Validate file path and check data integrity.""" if not Path(value).exists(): - msg = "File path does not exists!! Please do check path again" + msg = "File path does not exist! Please check the path again." raise ValueError(msg) - if ( - Path(value).exists() - and not Path(value).name.startswith(".") - and Path(value).name.endswith(".csv") - ): - data = vaex.read_csv(Path(value)) - if data.shape[0] | data.shape[1] == 0: - msg = "data doesnot exists" + + file_ext = Path(value).suffix.lower() + + try: + if file_ext == ".csv": + table = pcsv.read_csv(str(value)) + elif file_ext == ".arrow": + with pa.memory_map(str(value), "r") as mfile: + table = pa.ipc.open_file(mfile).read_all() + elif file_ext == ".feather": + table = pa_feather.read_table(str(value)) + else: + msg = f"Unsupported file format: {file_ext}" raise ValueError(msg) - elif ( - Path(value).exists() - and not Path(value).name.startswith(".") - and Path(value).name.endswith(EXT) - ): - data = vaex.open(Path(value)) - if data.shape[0] | data.shape[1] == 0: - msg = "data doesnot exists" + # Validate table contents + if table.num_rows == 0 or table.num_columns == 0: + msg = f"No data found in the file: {value}" raise ValueError(msg) + except Exception as e: + msg = f"Error reading file '{value}': {e}" + raise ValueError(msg) + return value + @field_validator("geometry_type") + def validate_geometry_type(cls, value: str) -> str: + valid_types = {"Polygon", "Point"} + if value not in valid_types: + msg = f"Invalid geometry type. Expected one of {valid_types}." + raise ValueError(msg) + return value + + def get_coordinates(self) -> list[dict[str, Any]]: + """Generate coordinates using the specified geometry type.""" + if self.geometry_type == "Polygon": + spec = PolygonSpec( + stitch_path=self.stitch_path, + stitch_pattern=self.stitch_pattern, + group_by=self.group_by, + ) + elif self.geometry_type == "Point": + spec = PointSpec( + stitch_path=self.stitch_path, + stitch_pattern=self.stitch_pattern, + group_by=self.group_by, + ) + else: + msg = f"Unsupported geometry type: {self.geometry_type}" + raise ValueError(msg) + + return spec.get_coordinates() + @property def microjson_overlay(self) -> None: """Create microjson overlays in JSON Format.""" if self.file_path.name.endswith((".csv", ".feather", ".arrow")): - data = convert_vaex_dataframe(self.file_path) + data = ut.convert_pyarrow_dataframe(self.file_path) + des_columns = [ feature - for feature in data.get_column_names() - if data.data_type(feature) == str + for feature in data.column_names + if data[feature].type == pa.string() ] - int_columns = [ feature - for feature in data.get_column_names() - if data.data_type(feature) == int or data.data_type(feature) == float + for feature in data.column_names + if ( + data[feature].type == pa.int32() + or data[feature].type == pa.int64() + or data[feature].type == pa.float32() + or data[feature].type == pa.float64() + ) ] - if len(int_columns) == 0: msg = "Features with integer datatype do not exist" raise ValueError(msg) @@ -317,92 +270,63 @@ def microjson_overlay(self) -> None: msg = "Descriptive features do not exist" raise ValueError(msg) - data["geometry_type"] = np.repeat(self.geometry_type, data.shape[0]) - data["type"] = np.repeat("Feature", data.shape[0]) + # Adding new columns + geometry_col = pa.array(np.repeat(self.geometry_type, len(data))) + sub_geometry = pa.array(np.repeat("Rectangle", len(data))) + type_col = pa.array(np.repeat("Feature", len(data))) + + data = data.append_column("geometry_type", geometry_col) + data = data.append_column("sub_type", sub_geometry) + data = data.append_column("type", type_col) + + excolumns = ["geometry_type", "sub_type", "type"] - excolumns = ["geometry_type", "type"] + columns = [col for col in data.column_names if col not in excolumns] - des_columns = [col for col in des_columns if col not in excolumns] + datarows = (row for batch in data.to_batches() for row in batch.to_pylist()) + datarows = sorted(datarows, key=lambda x: x["intensity_image"]) features: list[mj.Feature] = [] - for d, cor in zip(data.iterrows(), self.coordinates): - _, row = d - if row["intensity_image"] == cor["file"]: - desc = [{key: row[key]} for key in des_columns] - nume = [{key: row[key]} for key in int_columns] - - descriptive_dict = {} - for sub_dict in desc: - descriptive_dict.update(sub_dict) - - numeric_dict = {} - for sub_dict in nume: - numeric_dict.update(sub_dict) - - GeometryClass = getattr(mj, row["geometry_type"]) # noqa: N806 - cor_value = ast.literal_eval(cor["coordinates"]) - geometry = GeometryClass( - type=row["geometry_type"], - coordinates=cor_value, - ) + coordinates = self.get_coordinates() - # create a new properties object dynamically - properties = ValidatedProperties( - string=descriptive_dict, - numeric=numeric_dict, - ) + for m in coordinates: + file, cor = m.get("file"), m.get("coordinates") - # Create a new Feature object - feature = mj.MicroFeature( - type=row["type"], - geometry=geometry, - properties=properties, - ) - features.append(feature) + row_feats = ut.get_row_features(file, datarows, columns) - valrange = [ - {i: {"min": data[i].min(), "max": data[i].max()}} for i in int_columns - ] - valrange_dict = {} - for sub_dict in valrange: - valrange_dict.update(sub_dict) + properties = {} + for sub_dict in row_feats: + properties.update(sub_dict) - # Create a list of descriptive fields - descriptive_fields = des_columns + GeometryClass = getattr(mj, self.geometry_type) # noqa: N806 + cor_value = ast.literal_eval(cor) + + geometry = GeometryClass( + type=self.geometry_type, + subtype="Rectangle", + coordinates=cor_value, + ) + feature = mj.MicroFeature( + type="Feature", + geometry=geometry, + properties=properties, + ) + + features.append(feature) # Create a new FeatureCollection object feature_collection = mj.MicroFeatureCollection( type="FeatureCollection", features=features, - value_range=valrange_dict, - descriptive_fields=descriptive_fields, - coordinatesystem={ - "axes": [ - { - "name": "x", - "unit": "micrometer", - "type": "cartesian", - "pixelsPerUnit": 1, - "description": "x-axis", - }, - { - "name": "y", - "unit": "micrometer", - "type": "cartesian", - "pixelsPerUnit": 1, - "description": "y-axis", - }, - ], - "origo": "top-left", - }, ) + out_name = Path(self.out_dir, f"{self.file_path.stem}_overlay.json") + if len(feature_collection.model_dump_json()) == 0: msg = "JSON file is empty" raise ValueError(msg) if len(feature_collection.model_dump_json()) > 0: - out_name = Path(self.out_dir, f"{self.file_path.stem}_overlay.json") with Path.open(out_name, "w") as f: f.write( feature_collection.model_dump_json( @@ -411,3 +335,7 @@ def microjson_overlay(self) -> None: ), ) logger.info(f"Saving overlay json file: {out_name}") + + if self.tile_json: + logger.info(f"Generating tileJSON: {out_name}") + ut.convert_microjson_tile_json(out_name) diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py new file mode 100644 index 000000000..2c8132682 --- /dev/null +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py @@ -0,0 +1,208 @@ +"""Render Overlay.""" +import logging +import os +from pathlib import Path +from typing import Any +from typing import Optional + +import filepattern as fp +import pyarrow as pa +import pyarrow.csv as pcsv +import pyarrow.feather as pa_feather +import pydantic +from microjson.tilemodel import TileJSON +from microjson.tilemodel import TileLayer +from microjson.tilemodel import TileModel +from microjson.tilewriter import TileWriter +from microjson.tilewriter import extract_fields_ranges_enums +from microjson.tilewriter import getbounds +from pydantic import field_validator + +logger = logging.getLogger(__name__) +logger.setLevel(logging.INFO) + +POLUS_TAB_EXT = os.environ.get("POLUS_TAB_EXT", ".csv") +EXT = (".arrow", ".feather") + + +def convert_pyarrow_dataframe(file_path: Path): + """The PyArrow reading of tabular data with (".csv", ".feather", ".arrow") format. + + Args: + file_path: Path to tabular data. + + Returns: + A PyArrow Table. + """ + if file_path.name.endswith(".csv"): + # Reading CSV file into a PyArrow Table + return pcsv.read_csv(str(file_path)) + if file_path.name.endswith(".feather"): + # Reading Feather file into a PyArrow Table + return pa_feather.read_table(str(file_path)) + if file_path.name.endswith(".arrow"): + # Reading Arrow file into a PyArrow Table + with pa.memory_map(str(file_path), "r") as mfile: + # Read the file as a Table + return pa.ipc.open_file(mfile).read_all() + + return None + + +def get_row_features( + file: str, datarows: list[dict[str, Optional[str]]], columns: list[str], +) -> list[dict[str, Optional[str]]]: + """Retrieves the features of all rows from 'datarows' that match the given 'file' based on the 'intensity_image' key. + If no matching rows are found, returns a list containing a single dictionary with 'None' values for each specified column. + + Args: + file: The intensity image filename to match against the 'intensity_image' key in 'datarows'. + datarows: A list of dictionaries representing rows, each containing string keys and optional string values. + columns: A list of column names to extract from the matching rows. + + Returns: + List: A list of dictionaries containing the features of the matching rows, or a single dictionary with 'None' for each column if no matches are found. + """ + matching_rows = [ + {key: row.get(key) for key in columns} + for row in datarows + if row.get("intensity_image") == file + ] + return matching_rows if matching_rows else [{key: None for key in columns}] + + +class BaseOverlayModel(pydantic.BaseModel): + """Setting up configuration for pydantic base model.""" + + class Config: + """Model configuration.""" + + extra = "allow" + allow_population_by_field_name = True + + +class StitchingValidator(BaseOverlayModel): + """Validate stiching vector path and stiching pattern fields. + + This validates values passed for stitch_path and stitch_pattern attributes. + + Args: + stitch_path: Path to the stitching vector, containing x and y image positions. + stitch_pattern: Pattern to parse image filenames in stitching vector. + + Returns: + Attribute values + + """ + + stitch_path: Path + stitch_pattern: str + + @field_validator("stitch_path") + def validate_stitch_path(cls, value: Path) -> Path: + """Validate stitch path.""" + if not Path(value).exists(): + msg = "Stitching path does not exists!! Please do check path again" + raise ValueError(msg) + + if not Path(value).is_file(): + msg = f"Stitching path is not a file: {value}" + raise ValueError(msg) + + with Path(value).open() as f: + if not f.readlines(): + msg = "Stitching vector is empty so grid positions cannot be defined" + raise ValueError(msg) + + return value + + @field_validator("stitch_pattern") + def validate_stitch_pattern(cls, value: str, info: Any) -> str: + """Validate stitch pattern based on stitch path.""" + stitch_path = info.data.get("stitch_path") + if not stitch_path: + msg = "stitch_path must be provided first." + raise ValueError(msg) + + # Example logic for validating the pattern + if not stitch_path.suffix: + msg = "stitch_path must point to a valid file with an extension." + raise ValueError(msg) + + # Replace this with the actual logic for validating the pattern + files = fp.FilePattern(stitch_path, value) + if len(files) == 0: + msg = "Unable to parse file with the provided stitch pattern." + raise ValueError(msg) + + return value + + +def convert_microjson_tile_json(microjson_path: Path) -> None: + """Converts a MicroJSON file to TileJSON format. + + Args: + microjson_path: Path to the input MicroJSON file. + + Outputs: + - A `metadata.json` file with TileJSON metadata. + - A `tiles` directory containing generated PBF tile files. + """ + if microjson_path: + # Extract fields, ranges, enums from the provided MicroJSON + field_names, field_ranges, field_enums = extract_fields_ranges_enums( + microjson_path, + ) + + # Create a TileLayer including the extracted fields + vector_layers = [ + TileLayer( + id="extracted-layer", + fields=field_names, + minzoom=0, + maxzoom=10, + description="Layer with extracted fields", + fieldranges=field_ranges, + fieldenums=field_enums, + ), + ] + + # # create the tiles directory + out_dir = Path(microjson_path.parent).joinpath("tiles") + + if not out_dir.exists(): + out_dir.mkdir(parents=True, exist_ok=True) + + # get bounds + maxbounds = getbounds(microjson_path) + + center = [ + 0, + (maxbounds[0] + maxbounds[2]) / 2, + (maxbounds[1] + maxbounds[3]) / 2, + ] + + # Instantiate TileModel with your settings + tile_model = TileModel( + tilejson="3.0.0", + tiles=["tiles/{z}/{x}/{y}.pbf"], # Local path or URL + name="Example Tile Layer", + description="A TileJSON example incorporating MicroJSON data", + version="1.0.0", + attribution="Polus AI", + minzoom=0, + maxzoom=7, + bounds=maxbounds, + center=center, + vector_layers=vector_layers, + ) + + # Create the root model with your TileModel instance + tileobj = TileJSON(root=tile_model) + + with Path.open(out_dir.joinpath("metadata.json"), "w") as f: + f.write(tileobj.model_dump_json(indent=2)) + + # Initialize the TileHandler + handler = TileWriter(tile_model, pbf=True) + handler.microjson2tiles(microjson_path, validate=False) From c53ee683a9f68562a8c744747f6f854515bf555e Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Mon, 27 Jan 2025 13:45:11 -0500 Subject: [PATCH 2/5] updated test and documentations --- .../.bumpversion.cfg | 2 +- .../tabular-to-microjson-tool/README.md | 6 +- .../tabular-to-microjson-tool/VERSION | 2 +- .../examples/example_overlay_Point.json | 9255 --------- .../examples/example_overlay_Polygon.json | 16935 ---------------- .../tabular-to-microjson-tool/ict.yaml | 17 +- .../tabular-to-microjson-tool/plugin.json | 18 +- .../tabular-to-microjson-tool/pyproject.toml | 2 +- .../tabular-to-microjson-tool/run-plugin.sh | 5 +- .../tabular_to_microjson/__init__.py | 2 +- .../tabular_to_microjson/__main__.py | 37 +- .../tabular_to_microjson/microjson_overlay.py | 22 +- .../tabular_to_microjson/utils.py | 120 +- .../tabulartomicrojson.cwl | 6 +- .../tests/test_microjson_overlay.py | 61 +- 15 files changed, 212 insertions(+), 26278 deletions(-) delete mode 100644 visualization/tabular-to-microjson-tool/examples/example_overlay_Point.json delete mode 100644 visualization/tabular-to-microjson-tool/examples/example_overlay_Polygon.json diff --git a/visualization/tabular-to-microjson-tool/.bumpversion.cfg b/visualization/tabular-to-microjson-tool/.bumpversion.cfg index db24dbe12..ff4f9a49f 100644 --- a/visualization/tabular-to-microjson-tool/.bumpversion.cfg +++ b/visualization/tabular-to-microjson-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.3 +current_version = 0.1.4-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/visualization/tabular-to-microjson-tool/README.md b/visualization/tabular-to-microjson-tool/README.md index 3d1b5a731..1d45d45e1 100644 --- a/visualization/tabular-to-microjson-tool/README.md +++ b/visualization/tabular-to-microjson-tool/README.md @@ -1,4 +1,4 @@ -# Tabular To Microjson(v0.1.1) +# Tabular To Microjson(v0.1.4-dev0) This plugin uses [MICROJSON](https://github.com/bengtl/microjson/tree/dev) python library to generate JSON from tabular data which can be used in [RENDER UI](https://render.ci.ncats.io/?imageUrl=https://files.scb-ncats.io/pyramids/Idr0033/precompute/41744/x(00-15)_y(01-24)_p0(1-9)_c(1-5)/) @@ -10,7 +10,7 @@ Note: The filenames of tabular and stitching vector should be same Note: Currently this plugin supports two geometry types `Polygon` and `Point`.A future work requires additional support of more geometry types in this plugin. -Currently this plugins handles only three file formats supported by vaex. +Currently this plugins handles only three file formats supported by pyarrow. 1. csv 2. arrow 3. feather @@ -42,6 +42,7 @@ This plugin can take seven input arguments and one output argument: | `stitchPattern` | Pattern to parse filenames in stitching vector | Input | string | | `groupBy` | Variable to group filenames in stitching vector | Input | string | | `geometryType` | Geometry type (Polygon, Point) | Input | string | +| `tileJson` | TileJSON layer | Input | boolean | | `outDir` | Output directory for overlays | Output | string | | `preview` | Generate a JSON file with outputs | Output | JSON | @@ -57,6 +58,7 @@ docker run -v /data:/data polusai/tabular-to-microjson-plugin:0.1.1 \ --stitchPattern "x{x:dd}_y{y:dd}_c{c:d}.ome.tif" \ --groupBy None \ --geometryType "Polygon" \ + --tileJson \ --outDir /data/output \ --preview ``` diff --git a/visualization/tabular-to-microjson-tool/VERSION b/visualization/tabular-to-microjson-tool/VERSION index b1e80bb24..197c2b5ee 100644 --- a/visualization/tabular-to-microjson-tool/VERSION +++ b/visualization/tabular-to-microjson-tool/VERSION @@ -1 +1 @@ -0.1.3 +0.1.4-dev0 diff --git a/visualization/tabular-to-microjson-tool/examples/example_overlay_Point.json b/visualization/tabular-to-microjson-tool/examples/example_overlay_Point.json deleted file mode 100644 index 3c442063b..000000000 --- a/visualization/tabular-to-microjson-tool/examples/example_overlay_Point.json +++ /dev/null @@ -1,9255 +0,0 @@ -{ - "type": "FeatureCollection", - "features": 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"Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 20867.0, - "maxVirusIntensity": 14361.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 32550.0, - 32550.0 - ], - [ - 34730.0, - 32550.0 - ], - [ - 34730.0, - 34730.0 - ], - [ - 32550.0, - 34730.0 - ], - [ - 32550.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P16", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 21680.0, - "maxVirusIntensity": 8615.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 34720.0, - 32550.0 - ], - [ - 36900.0, - 32550.0 - ], - [ - 36900.0, - 34730.0 - ], - [ - 34720.0, - 34730.0 - ], - [ - 34720.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P17", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 20463.0, - "maxVirusIntensity": 14900.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 36890.0, - 32550.0 - ], - [ - 39070.0, - 32550.0 - ], - [ - 39070.0, - 34730.0 - ], - [ - 36890.0, - 34730.0 - ], - [ - 36890.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P18", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 17918.0, - "maxVirusIntensity": 8334.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 39060.0, - 32550.0 - ], - [ - 41240.0, - 32550.0 - ], - [ - 41240.0, - 34730.0 - ], - [ - 39060.0, - 34730.0 - ], - [ - 39060.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P19", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 18390.0, - "maxVirusIntensity": 10395.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 41230.0, - 32550.0 - ], - [ - 43410.0, - 32550.0 - ], - [ - 43410.0, - 34730.0 - ], - [ - 41230.0, - 34730.0 - ], - [ - 41230.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P20", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 22646.0, - "maxVirusIntensity": 17977.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 43400.0, - 32550.0 - ], - [ - 45580.0, - 32550.0 - ], - [ - 45580.0, - 34730.0 - ], - [ - 43400.0, - 34730.0 - ], - [ - 43400.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P21", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 17558.0, - "maxVirusIntensity": 15061.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 45570.0, - 32550.0 - ], - [ - 47750.0, - 32550.0 - ], - [ - 47750.0, - 34730.0 - ], - [ - 45570.0, - 34730.0 - ], - [ - 45570.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P22", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 18997.0, - "maxVirusIntensity": 16450.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 47740.0, - 32550.0 - ], - [ - 49920.0, - 32550.0 - ], - [ - 49920.0, - 34730.0 - ], - [ - 47740.0, - 34730.0 - ], - [ - 47740.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P23", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 18777.0, - "maxVirusIntensity": 26002.0 - } - } - }, - { - "type": "Feature", - "geometry": { - "type": "Polygon", - "coordinates": [ - [ - [ - 49910.0, - 32550.0 - ], - [ - 52090.0, - 32550.0 - ], - [ - 52090.0, - 34730.0 - ], - [ - 49910.0, - 34730.0 - ], - [ - 49910.0, - 32550.0 - ] - ] - ] - }, - "properties": { - "string": { - "Plate": "preZ", - "Well": "P24", - "Characteristics [Organism 2]": "Herpes simplex virus type 1", - "Characteristics [Cell Line]": "A549", - "Compound Name": "Ganciclovir", - "Control Type": "positive control" - }, - "numeric": { - "numberOfNuclei": 18082.0, - "maxVirusIntensity": 30486.0 - } - } - } - ], - "coordinatesystem": { - "axes": [ - { - "name": "x", - "type": "cartesian", - "unit": "micrometer", - "description": "x-axis" - }, - { - "name": "y", - "type": "cartesian", - "unit": "micrometer", - "description": "y-axis" - } - ] - }, - "value_range": { - "numberOfNuclei": { - "min": 16728.0, - "max": 29288.0 - }, - "maxVirusIntensity": { - "min": 5615.0, - "max": 65535.0 - } - }, - "descriptive_fields": [ - "Plate", - "Well", - "Characteristics [Organism 2]", - "Characteristics [Cell Line]", - "Compound Name", - "Control Type" - ] -} diff --git a/visualization/tabular-to-microjson-tool/ict.yaml b/visualization/tabular-to-microjson-tool/ict.yaml index c962e9c54..377a5e19c 100644 --- a/visualization/tabular-to-microjson-tool/ict.yaml +++ b/visualization/tabular-to-microjson-tool/ict.yaml @@ -1,7 +1,7 @@ author: - Hamdah Shafqat contact: hamdahshafqat.abbasi@nih.gov -container: polusai/tabular-to-microjson-tool:0.1.2-dev0 +container: polusai/tabular-to-microjson-tool:0.1.4-dev0 description: Generates JSON from tabular data. entrypoint: python3 -m polus.images.visualization.tabular_to_microjson inputs: @@ -35,6 +35,12 @@ inputs: name: groupBy required: false type: string +- description: TileJSON layer + format: + - boolean + name: tileJson + required: false + type: boolean - description: Type of geometry coordinates format: - string @@ -49,7 +55,7 @@ outputs: name: outDir required: true type: path -repository: https://github.com/PolusAI/polus-plugins +repository: https://github.com/PolusAI/image-tools specVersion: 1.0.0 title: Tabular To Microjson ui: @@ -77,4 +83,9 @@ ui: key: inputs.geometryType title: geometryType type: text -version: 0.1.2-dev0 +- default: false + description: TileJSON layer + key: inputs.tileJson + title: tileJson + type: checkbox +version: 0.1.4-dev0 diff --git a/visualization/tabular-to-microjson-tool/plugin.json b/visualization/tabular-to-microjson-tool/plugin.json index b3951becd..00a398aac 100644 --- a/visualization/tabular-to-microjson-tool/plugin.json +++ b/visualization/tabular-to-microjson-tool/plugin.json @@ -1,12 +1,12 @@ { "name": "Tabular To Microjson", - "version": "0.1.3", - "containerId": "polusai/tabular-to-microjson-tool:0.1.3", + "version": "0.1.4-dev0", + "containerId": "polusai/tabular-to-microjson-tool:0.1.4-dev0", "title": "Tabular To Microjson", "description": "Generates JSON from tabular data.", "author": "Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", "institution": "National Center for Advancing Translational Sciences, National Institutes of Health", - "repository": "https://github.com/PolusAI/polus-plugins", + "repository": "https://github.com/PolusAI/image-tools", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", "baseCommand": [ @@ -45,6 +45,12 @@ "type": "string", "required": false }, + { + "name": "tileJson", + "description": "TileJSON layer", + "type": "boolean", + "required": false + }, { "name": "geometryType", "description": "Type of geometry coordinates", @@ -91,6 +97,12 @@ "title": "geometryType", "description": "Type of geometry coordinates", "default": "Polygon" + }, + { + "key": "inputs.tileJson", + "title": "tileJson", + "description": "TileJSON layer", + "default": false } ] } diff --git a/visualization/tabular-to-microjson-tool/pyproject.toml b/visualization/tabular-to-microjson-tool/pyproject.toml index 1ef592ff8..6e5be2db3 100644 --- a/visualization/tabular-to-microjson-tool/pyproject.toml +++ b/visualization/tabular-to-microjson-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-images-visualization-tabular-to-microjson" -version = "0.1.3" +version = "0.1.4-dev0" description = "" authors = ["Hamdah Shafqat abbasi "] readme = "README.md" diff --git a/visualization/tabular-to-microjson-tool/run-plugin.sh b/visualization/tabular-to-microjson-tool/run-plugin.sh index d3f055c91..e3be75542 100644 --- a/visualization/tabular-to-microjson-tool/run-plugin.sh +++ b/visualization/tabular-to-microjson-tool/run-plugin.sh @@ -14,15 +14,14 @@ group_by=None out_dir=${datapath}/output -# # # Show the help options -# # # docker run polusai/tabular-to-microjson-plugin:${version} docker run -v ${datapath}:${datapath} \ - polusai/tabular-to-microjson-plugin:${version} \ + polusai/tabular-to-microjson-tool:${version} \ --inpDir ${inp_dir} \ --stitchDir ${stitch_dir} \ --filePattern ${file_pattern} \ --stitchPattern ${stitch_pattern} \ --groupBy ${group_by} \ --geometryType ${geometry_type} \ + --tileJson \ --outDir ${out_dir} diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py index 24ef5bb9d..148593ccb 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py @@ -1,2 +1,2 @@ """Tabular to microjson package.""" -__version__ = "0.1.3" +__version__ = "0.1.4-dev0" diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py index d90f79e24..5308f6ab5 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py @@ -1,14 +1,15 @@ """Tabular to microjson package.""" + import logging import os import pathlib -import shutil import warnings from concurrent.futures import ThreadPoolExecutor from multiprocessing import cpu_count from typing import Optional import filepattern as fp +import polus.images.visualization.tabular_to_microjson.utils as ut import typer from polus.images.visualization.tabular_to_microjson import microjson_overlay as mo from tqdm import tqdm @@ -96,26 +97,22 @@ def main( # noqa: PLR0913 st for st in stitch_dir.iterdir() if st.suffix == ".txt" and st.is_file() ][0] - with ThreadPoolExecutor(max_workers=num_workers) as executor: - for file in tqdm(files, desc="Creating overlays", total=len(files)): - micro_model = mo.RenderOverlayModel( - file_path=file, - geometry_type=geometry_type, - stitch_path=stitch_path, - stitch_pattern=stitch_pattern, - group_by=group_by, - tile_json=tile_json, - out_dir=out_dir, - ) - executor.submit(micro_model.microjson_overlay) + if not preview: + with ThreadPoolExecutor(max_workers=num_workers) as executor: + for file in tqdm(files, desc="Creating overlays", total=len(files)): + micro_model = mo.RenderOverlayModel( + file_path=file, + geometry_type=geometry_type, + stitch_path=stitch_path, + stitch_pattern=stitch_pattern, + group_by=group_by, + tile_json=tile_json, + out_dir=out_dir, + ) + executor.submit(micro_model.microjson_overlay) - if preview: - shutil.copy( - pathlib.Path(__file__) - .parents[5] - .joinpath(f"examples/example_overlay_{geometry_type}.json"), - out_dir, - ) + else: + ut.preview_data(out_dir) if __name__ == "__main__": diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py index 583a94c5f..83820e690 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py @@ -1,4 +1,5 @@ """Render Overlay.""" + import ast import logging import os @@ -102,8 +103,8 @@ class PointSpec(ut.StitchingValidator): Returns: A list of dictionaries, each containing: - - "file": The parsed filename. - - "coordinates": A tuple representing the centroid of the calculated rectangle. + - file: The parsed filename. + - coordinates: A tuple for the centroid of the rectangle. """ @@ -173,7 +174,8 @@ class RenderOverlayModel(ut.StitchingValidator): file_path: Path = Field(..., description="Input file path.") geometry_type: str = Field( - ..., description="Type of geometry: 'polygon' or 'point'", + ..., + description="Type of geometry: 'polygon' or 'point'", ) stitch_path: Path stitch_pattern: str @@ -207,14 +209,15 @@ def validate_file_path(cls, value: Path) -> Path: # noqa: N805 msg = f"No data found in the file: {value}" raise ValueError(msg) - except Exception as e: + except FileNotFoundError as e: msg = f"Error reading file '{value}': {e}" - raise ValueError(msg) + raise ValueError(msg) from None return value @field_validator("geometry_type") - def validate_geometry_type(cls, value: str) -> str: + def validate_geometry_type(cls, value: str) -> str: # noqa: N805 + """Validate geometry.""" valid_types = {"Polygon", "Point"} if value not in valid_types: msg = f"Invalid geometry type. Expected one of {valid_types}." @@ -284,7 +287,10 @@ def microjson_overlay(self) -> None: columns = [col for col in data.column_names if col not in excolumns] datarows = (row for batch in data.to_batches() for row in batch.to_pylist()) - datarows = sorted(datarows, key=lambda x: x["intensity_image"]) + datarows = sorted( + datarows, + key=lambda x: x["intensity_image"], + ) # type:ignore features: list[mj.Feature] = [] @@ -300,7 +306,7 @@ def microjson_overlay(self) -> None: properties.update(sub_dict) GeometryClass = getattr(mj, self.geometry_type) # noqa: N806 - cor_value = ast.literal_eval(cor) + cor_value = ast.literal_eval(cor) # type: ignore geometry = GeometryClass( type=self.geometry_type, diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py index 2c8132682..679679893 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py @@ -1,6 +1,9 @@ """Render Overlay.""" + +import json import logging import os +from collections.abc import Sequence from pathlib import Path from typing import Any from typing import Optional @@ -16,6 +19,7 @@ from microjson.tilewriter import TileWriter from microjson.tilewriter import extract_fields_ranges_enums from microjson.tilewriter import getbounds +from pydantic import PydanticModelField from pydantic import field_validator logger = logging.getLogger(__name__) @@ -25,7 +29,7 @@ EXT = (".arrow", ".feather") -def convert_pyarrow_dataframe(file_path: Path): +def convert_pyarrow_dataframe(file_path: Path) -> None: """The PyArrow reading of tabular data with (".csv", ".feather", ".arrow") format. Args: @@ -50,18 +54,19 @@ def convert_pyarrow_dataframe(file_path: Path): def get_row_features( - file: str, datarows: list[dict[str, Optional[str]]], columns: list[str], + file: str, + datarows: list[dict[str, Optional[str]]], + columns: list[str], ) -> list[dict[str, Optional[str]]]: - """Retrieves the features of all rows from 'datarows' that match the given 'file' based on the 'intensity_image' key. - If no matching rows are found, returns a list containing a single dictionary with 'None' values for each specified column. + """Retrieves 'datarows' features matching the 'file' by 'intensity_image'. Args: - file: The intensity image filename to match against the 'intensity_image' key in 'datarows'. - datarows: A list of dictionaries representing rows, each containing string keys and optional string values. + file: The intensity image filename to match the intensity_image key in datarows. + datarows: A list of dictionaries with string keys and optional string values. columns: A list of column names to extract from the matching rows. Returns: - List: A list of dictionaries containing the features of the matching rows, or a single dictionary with 'None' for each column if no matches are found. + A list of matching rows or a dictionary with 'None' if no matches.. """ matching_rows = [ {key: row.get(key) for key in columns} @@ -99,7 +104,7 @@ class StitchingValidator(BaseOverlayModel): stitch_pattern: str @field_validator("stitch_path") - def validate_stitch_path(cls, value: Path) -> Path: + def validate_stitch_path(cls, value: Path) -> Path: # noqa: N805 """Validate stitch path.""" if not Path(value).exists(): msg = "Stitching path does not exists!! Please do check path again" @@ -113,23 +118,24 @@ def validate_stitch_path(cls, value: Path) -> Path: if not f.readlines(): msg = "Stitching vector is empty so grid positions cannot be defined" raise ValueError(msg) - return value @field_validator("stitch_pattern") - def validate_stitch_pattern(cls, value: str, info: Any) -> str: + def validate_stitch_pattern( + cls, # noqa: N805 + value: str, + info: PydanticModelField, + ) -> str: """Validate stitch pattern based on stitch path.""" stitch_path = info.data.get("stitch_path") if not stitch_path: msg = "stitch_path must be provided first." raise ValueError(msg) - # Example logic for validating the pattern if not stitch_path.suffix: msg = "stitch_path must point to a valid file with an extension." raise ValueError(msg) - # Replace this with the actual logic for validating the pattern files = fp.FilePattern(stitch_path, value) if len(files) == 0: msg = "Unable to parse file with the provided stitch pattern." @@ -206,3 +212,93 @@ def convert_microjson_tile_json(microjson_path: Path) -> None: # Initialize the TileHandler handler = TileWriter(tile_model, pbf=True) handler.microjson2tiles(microjson_path, validate=False) + + +def create_example_microjson( + features_data: list[dict[str, Any]], +) -> dict[str, Sequence[str]]: + """Create a MicroJSON FeatureCollection from a list of feature data. + + Args: + features_data: A list of dictionaries containing data for each feature. + + Returns: + A MicroJSON FeatureCollection. + """ + micro_json = {"type": "FeatureCollection", "features": []} + + for feature in features_data: + geometry = {"type": "Polygon", "coordinates": [feature["coordinates"]]} + + properties = { + key: value for key, value in feature.items() if key not in ["coordinates"] + } + + micro_json["features"].append( # type: ignore + {"type": "Feature", "geometry": geometry, "properties": properties}, + ) + + return micro_json + + +def preview_data(out_dir: Path) -> None: + """Create a example MicroJSON FeatureCollection from a list of feature data.""" + features_data = [ + { + "coordinates": [ + [0.0, 0.0], + [1034.0, 0.0], + [1034.0, 1034.0], + [0.0, 1034.0], + [0.0, 0.0], + ], + "experiment": "ncgca-sod1-p1 ck180618n1", + "row_number": 1, + "col_number": 1, + "well": "A01", + "plate": "CD_SOD1_2_E1023884__1", + "neg_controls": 1, + "pos_controls": 0, + "intensity_image": "x00_y01_c0.ome.tif", + "Count": 333, + "FPR": 0.0390, + "OTSU": 0.195, + "NSIGMA": 0.024, + }, + { + "coordinates": [ + [1034.0, 0.0], + [2068.0, 0.0], + [2068.0, 1034.0], + [1034.0, 1034.0], + [1034.0, 0.0], + ], + "experiment": "ncgca-sod1-p1 ck180618n1", + "row_number": 1, + "col_number": 2, + "well": "A02", + "plate": "CD_SOD1_2_E1023884__1", + "neg_controls": 0, + "pos_controls": 0, + "intensity_image": "x00_y02_c0.ome.tif", + "Count": 363, + "FPR": 0.190, + "OTSU": 0.413, + "NSIGMA": 0.123, + }, + { + "coordinates": [ + [2068.0, 0.0], + [3102.0, 0.0], + [3102.0, 1034.0], + [2068.0, 1034.0], + [2068.0, 0.0], + ], + }, + ] + + microjson_output = create_example_microjson(features_data) # type: ignore + out_file = out_dir.joinpath("example_data.json") + + with Path.open(out_file, "w") as json_file: + json.dump(microjson_output, json_file, indent=2) diff --git a/visualization/tabular-to-microjson-tool/tabulartomicrojson.cwl b/visualization/tabular-to-microjson-tool/tabulartomicrojson.cwl index 2e2d5c4da..8f9970c4d 100644 --- a/visualization/tabular-to-microjson-tool/tabulartomicrojson.cwl +++ b/visualization/tabular-to-microjson-tool/tabulartomicrojson.cwl @@ -29,6 +29,10 @@ inputs: inputBinding: prefix: --stitchPattern type: string + tileJson: + inputBinding: + prefix: --tileJson + type: boolean? outputs: outDir: outputBinding: @@ -36,7 +40,7 @@ outputs: type: Directory requirements: DockerRequirement: - dockerPull: polusai/tabular-to-microjson-tool:0.1.2-dev0 + dockerPull: polusai/tabular-to-microjson-tool:0.1.4-dev0 InitialWorkDirRequirement: listing: - entry: $(inputs.outDir) diff --git a/visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py b/visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py index 7e8d7d88d..bfa0df378 100644 --- a/visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py +++ b/visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py @@ -1,4 +1,6 @@ """Test for tabular to microjson package.""" + +import ast import json import pathlib import shutil @@ -6,9 +8,11 @@ import tempfile import numpy as np -import pandas as pd +import polus.images.visualization.tabular_to_microjson.utils as ut +import pyarrow as pa +import pyarrow.csv as pcsv +import pyarrow.feather as pa_feather import pytest -import vaex from polus.images.visualization.tabular_to_microjson import microjson_overlay as mo from polus.images.visualization.tabular_to_microjson.__main__ import app from typer.testing import CliRunner @@ -31,7 +35,7 @@ def input_directory() -> pathlib.Path: def clean_directories() -> None: """Remove all temporary directories.""" for d in pathlib.Path(".").cwd().iterdir(): - if d.is_dir() and d.name.startswith("tmp"): + if d.is_dir() and d.name.startswith("tmp") or d.name.startswith("tiles"): shutil.rmtree(d) @@ -51,7 +55,7 @@ def generate_synthetic_data( get_params: tuple[int, int, str, str], ) -> tuple[pathlib.Path, pathlib.Path]: """Generate tabular data.""" - nrows, cell_width, geometry_type, file_extension = get_params + nrows, cell_width, _, file_extension = get_params n = int(nrows / 384) rng = np.random.default_rng(42) @@ -108,29 +112,31 @@ def generate_synthetic_data( ), } - df = pd.DataFrame(diction_1) + table = pa.Table.from_pydict(diction_1) if file_extension == ".csv": outpath = pathlib.Path(input_directory, "data/data.csv") - df.to_csv(outpath, index=False) + pcsv.write_csv(table, outpath) if file_extension == ".feather": outpath = pathlib.Path(input_directory, "data/data.feather") - df.to_feather(outpath) + pa_feather.write_feather(table, outpath) if file_extension == ".arrow": outpath = pathlib.Path(input_directory, "data/data.arrow") - df.to_feather(outpath) + with pa.OSFile(outpath, "wb") as outarrow: + writer = pa.ipc.new_file(outarrow, table.schema) + writer.write(table) + writer.close() return outpath, stitch_path -def test_convert_vaex_dataframe( +def test_convert_pyarrow_dataframe( generate_synthetic_data: tuple[pathlib.Path, pathlib.Path], ) -> None: """Converting tabular data to vaex dataframe.""" outpath, _ = generate_synthetic_data - vaex_df = mo.convert_vaex_dataframe(outpath) - assert type(vaex_df) == vaex.dataframe.DataFrameLocal - assert len(list(vaex_df.columns)) != 0 - assert vaex_df.shape[0] > 0 + pyarrow_df = ut.convert_pyarrow_dataframe(outpath) + assert len(list(pyarrow_df.columns)) != 0 + assert pyarrow_df.shape[0] > 0 clean_directories() @@ -147,8 +153,9 @@ def test_generate_polygon_coordinates( stitch_pattern=stitch_pattern, group_by=group_by, ) - poly = model.get_coordinates - assert all(len(i) for p in poly[0]["coordinates"] for i in p) is True + poly = model.get_coordinates() + coordinates_list = [ast.literal_eval(item["coordinates"])[0] for item in poly] + assert all(len(i) for i in coordinates_list) is True clean_directories() @@ -164,7 +171,7 @@ def test_generate_rectangular_polygon_centroids( stitch_pattern=stitch_pattern, group_by=group_by, ) - poly = model.get_coordinates + poly = model.get_coordinates() expected_len = 2 assert len(poly[0]["coordinates"]) == expected_len clean_directories() @@ -180,26 +187,15 @@ def test_render_overlay_model( stitch_pattern = "x{x:dd}_y{y:dd}_p{p:d}_c{c:d}.ome.tif" _, _, geometry_type, _ = get_params group_by = None - - if geometry_type == "Polygon": - model = mo.PolygonSpec( - stitch_path=str(stitch_dir), - stitch_pattern=stitch_pattern, - group_by=group_by, - ) - - if geometry_type == "Point": - model = mo.PointSpec( - stitch_path=str(stitch_dir), - stitch_pattern=stitch_pattern, - group_by=group_by, - ) - poly = model.get_coordinates + tile_json = False microjson = mo.RenderOverlayModel( file_path=inp_dir, - coordinates=poly, geometry_type=geometry_type, + stitch_path=str(stitch_dir), + stitch_pattern=stitch_pattern, + group_by=group_by, + tile_json=tile_json, out_dir=output_directory, ) mjson = microjson.microjson_overlay @@ -236,6 +232,7 @@ def test_cli( None, "--geometryType", geometry_type, + "--tileJson", "--outDir", pathlib.Path(output_directory), ], From 8de106ae27f52441626125c552d3cbabb1fd38ce Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Mon, 27 Jan 2025 14:27:43 -0500 Subject: [PATCH 3/5] disable ruff check --- .../polus/images/visualization/tabular_to_microjson/utils.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py index 679679893..5b8f9a4f4 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py @@ -19,7 +19,6 @@ from microjson.tilewriter import TileWriter from microjson.tilewriter import extract_fields_ranges_enums from microjson.tilewriter import getbounds -from pydantic import PydanticModelField from pydantic import field_validator logger = logging.getLogger(__name__) @@ -124,7 +123,7 @@ def validate_stitch_path(cls, value: Path) -> Path: # noqa: N805 def validate_stitch_pattern( cls, # noqa: N805 value: str, - info: PydanticModelField, + info: Any, # noqa: ANN401 ) -> str: """Validate stitch pattern based on stitch path.""" stitch_path = info.data.get("stitch_path") From 69a4db54c0d176e9325a47918df244e6501d1014 Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Mon, 27 Jan 2025 14:51:57 -0500 Subject: [PATCH 4/5] updated python version and base container --- visualization/tabular-to-microjson-tool/Dockerfile | 2 +- visualization/tabular-to-microjson-tool/pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/visualization/tabular-to-microjson-tool/Dockerfile b/visualization/tabular-to-microjson-tool/Dockerfile index f8ff1aebd..70bdd5050 100644 --- a/visualization/tabular-to-microjson-tool/Dockerfile +++ b/visualization/tabular-to-microjson-tool/Dockerfile @@ -1,4 +1,4 @@ -FROM polusai/bfio:2.1.9 +FROM polusai/bfio:2.4.7 # environment variables defined in polusai/bfio ENV EXEC_DIR="/opt/executables" diff --git a/visualization/tabular-to-microjson-tool/pyproject.toml b/visualization/tabular-to-microjson-tool/pyproject.toml index 6e5be2db3..5fe859393 100644 --- a/visualization/tabular-to-microjson-tool/pyproject.toml +++ b/visualization/tabular-to-microjson-tool/pyproject.toml @@ -7,7 +7,7 @@ readme = "README.md" packages = [{include = "polus", from = "src"}] [tool.poetry.dependencies] -python = "<3.12,>=3.9.15" +python = "<3.12,>=3.10" typer = "^0.7.0" filepattern = "^2.0.1" tqdm = "^4.65.0" From 43fb6268ae6e0d54df5c6c90f5384f21f06fb8d5 Mon Sep 17 00:00:00 2001 From: Hamdah Shafqat Abbasi Date: Wed, 19 Feb 2025 15:23:38 -0500 Subject: [PATCH 5/5] fix tilepath --- .../images/visualization/tabular_to_microjson/utils.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py index 5b8f9a4f4..036a6b3f0 100644 --- a/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/utils.py @@ -190,7 +190,7 @@ def convert_microjson_tile_json(microjson_path: Path) -> None: # Instantiate TileModel with your settings tile_model = TileModel( tilejson="3.0.0", - tiles=["tiles/{z}/{x}/{y}.pbf"], # Local path or URL + tiles=["{z}/{x}/{y}.pbf"], # Local path or URL name="Example Tile Layer", description="A TileJSON example incorporating MicroJSON data", version="1.0.0", @@ -205,11 +205,13 @@ def convert_microjson_tile_json(microjson_path: Path) -> None: # Create the root model with your TileModel instance tileobj = TileJSON(root=tile_model) - with Path.open(out_dir.joinpath("metadata.json"), "w") as f: + tilepath = out_dir.joinpath("metadata.json") + with Path.open(tilepath, "w") as f: f.write(tileobj.model_dump_json(indent=2)) - # Initialize the TileHandler + # # Initialize the TileHandler handler = TileWriter(tile_model, pbf=True) + os.chdir(tilepath.parent) handler.microjson2tiles(microjson_path, validate=False)