atdata 0.1.2a4__py3-none-any.whl → 0.1.3a2__py3-none-any.whl

atdata/__init__.py

@@ -10,5 +10,11 @@ from .dataset import (
     packable,
 )
 
+from .lens import (
+    Lens,
+    LensNetwork,
+    lens,
+)
+
 
 #

atdata/dataset.py

@@ -5,21 +5,29 @@
 
 import webdataset as wds
 
-import functools
-from dataclasses import dataclass
+from pathlib import Path
 import uuid
-
-import numpy as np
-
+import functools
+from dataclasses import (
+    dataclass,
+    asdict,
+)
 from abc import (
     ABC,
     abstractmethod,
 )
+
+from tqdm import tqdm
+import numpy as np
+import pandas as pd
+
 from typing import (
     Any,
     Optional,
     Dict,
     Sequence,
+    Iterable,
+    Callable,
     #
     Self,
     Generic,
@@ -40,14 +48,20 @@ from numpy.typing import (
 import msgpack
 import ormsgpack
 from . import _helpers as eh
+from .lens import Lens, LensNetwork
 
 
 ##
 # Typing help
 
+Pathlike = str | Path
+
 WDSRawSample: TypeAlias = Dict[str, Any]
 WDSRawBatch: TypeAlias = Dict[str, Any]
 
+SampleExportRow: TypeAlias = Dict[str, Any]
+SampleExportMap: TypeAlias = Callable[['PackableSample'], SampleExportRow]
+
 
 ##
 # Main base classes
@@ -94,6 +108,7 @@ def _make_packable( x ):
         return eh.array_to_bytes( x )
     return x
 
+@dataclass
 class PackableSample( ABC ):
     """A sample that can be packed and unpacked with msgpack"""
 
@@ -217,6 +232,8 @@ class SampleBatch( Generic[DT] ):
 ST = TypeVar( 'ST', bound = PackableSample )
 # BT = TypeVar( 'BT' )
 
+RT = TypeVar( 'RT', bound = PackableSample )
+
 # TODO For python 3.13
 # BT = TypeVar( 'BT', default = None )
 # IT = TypeVar( 'IT', default = Any )
@@ -235,6 +252,7 @@ class Dataset( Generic[ST] ):
     @property
     def sample_type( self ) -> Type:
         """The type of each returned sample from this `Dataset`'s iterator"""
+        # TODO Figure out why linting fails here
         return self.__orig_class__.__args__[0]
     @property
     def batch_type( self ) -> Type:
@@ -253,6 +271,17 @@ class Dataset( Generic[ST] ):
         super().__init__()
         self.url = url
 
+        # Allow addition of automatic transformation of raw underlying data
+        self._output_lens: Lens | None = None
+
+    def as_type( self, other: Type[RT] ) -> 'Dataset[RT]':
+        """TODO"""
+        ret = Dataset[other]( self.url )
+        # Get the singleton lens registry
+        lenses = LensNetwork()
+        ret._output_lens = lenses.transform( self.sample_type, ret.sample_type )
+        return ret
+
     # @classmethod
     # def register( cls, uri: str,
     #             sample_class: Type,
@@ -278,15 +307,15 @@ class Dataset( Generic[ST] ):
             A full (non-lazy) list of the individual ``tar`` files within the
             source WebDataset.
         """
-        pipe = wds.DataPipeline(
-            wds.SimpleShardList( self.url ),
-            wds.map( lambda x: x['url'] )
+        pipe = wds.pipeline.DataPipeline(
+            wds.shardlists.SimpleShardList( self.url ),
+            wds.filters.map( lambda x: x['url'] )
         )
         return list( pipe )
     
     def ordered( self,
                 batch_size: int | None = 1,
-            ) -> wds.DataPipeline:
+            ) -> Iterable[ST]:
         """Iterate over the dataset in order
         
         Args:
@@ -302,30 +331,30 @@ class Dataset( Generic[ST] ):
 
         if batch_size is None:
             # TODO Duplication here
-            return wds.DataPipeline(
-                wds.SimpleShardList( self.url ),
-                wds.split_by_worker,
+            return wds.pipeline.DataPipeline(
+                wds.shardlists.SimpleShardList( self.url ),
+                wds.shardlists.split_by_worker,
                 #
-                wds.tarfile_to_samples(),
+                wds.tariterators.tarfile_to_samples(),
                 # wds.map( self.preprocess ),
-                wds.map( self.wrap ),
+                wds.filters.map( self.wrap ),
             )
 
-        return wds.DataPipeline(
-            wds.SimpleShardList( self.url ),
-            wds.split_by_worker,
+        return wds.pipeline.DataPipeline(
+            wds.shardlists.SimpleShardList( self.url ),
+            wds.shardlists.split_by_worker,
             #
-            wds.tarfile_to_samples(),
+            wds.tariterators.tarfile_to_samples(),
             # wds.map( self.preprocess ),
-            wds.batched( batch_size ),
-            wds.map( self.wrap_batch ),
+            wds.filters.batched( batch_size ),
+            wds.filters.map( self.wrap_batch ),
         )
 
     def shuffled( self,
                 buffer_shards: int = 100,
                 buffer_samples: int = 10_000,
                 batch_size: int | None = 1,
-            ) -> wds.DataPipeline:
+            ) -> Iterable[ST]:
         """Iterate over the dataset in random order
         
         Args:
@@ -366,6 +395,64 @@ class Dataset( Generic[ST] ):
             wds.batched( batch_size ),
             wds.map( self.wrap_batch ),
         )
+    
+    # TODO Rewrite to eliminate `pandas` dependency directly calling
+    # `fastparquet`
+    def to_parquet( self, path: Pathlike,
+                sample_map: Optional[SampleExportMap] = None,
+                maxcount: Optional[int] = None,
+                **kwargs,
+            ):
+        """Save dataset contents to a `parquet` file at `path`
+
+        `kwargs` sent to `pandas.to_parquet`
+        """
+        ##
+
+        # Normalize args
+        path = Path( path )
+        if sample_map is None:
+            sample_map = asdict
+        
+        verbose = kwargs.get( 'verbose', False )
+
+        it = self.ordered( batch_size = None )
+        if verbose:
+            it = tqdm( it )
+
+        #
+
+        if maxcount is None:
+            # Load and save full dataset
+            df = pd.DataFrame( [ sample_map( x )
+                                 for x in self.ordered( batch_size = None ) ] )
+            df.to_parquet( path, **kwargs )
+        
+        else:
+            # Load and save dataset in segments of size `maxcount`
+
+            cur_segment = 0
+            cur_buffer = []
+            path_template = (path.parent / f'{path.stem}-%06d.{path.suffix}').as_posix()
+
+            for x in self.ordered( batch_size = None ):
+                cur_buffer.append( sample_map( x ) )
+                
+                if len( cur_buffer ) >= maxcount:
+                    # Write current segment
+                    cur_path = path_template.format( cur_segment )
+                    df = pd.DataFrame( cur_buffer )
+                    df.to_parquet( cur_path, **kwargs )
+
+                    cur_segment += 1
+                    cur_buffer = []
+                
+            if len( cur_buffer ) > 0:
+                # Write one last segment with remainder
+                cur_path = path_template.format( cur_segment )
+                df = pd.DataFrame( cur_buffer )
+                df.to_parquet( cur_path, **kwargs )
+
 
     # Implemented by specific subclasses
 
@@ -388,20 +475,24 @@ class Dataset( Generic[ST] ):
         assert 'msgpack' in sample
         assert type( sample['msgpack'] ) == bytes
         
-        return self.sample_type.from_bytes( sample['msgpack'] )
+        if self._output_lens is None:
+            return self.sample_type.from_bytes( sample['msgpack'] )
+
+        source_sample = self._output_lens.source_type.from_bytes( sample['msgpack'] )
+        return self._output_lens( source_sample )
     
-        try:
-            assert type( sample ) == dict
-            return cls.sample_class( **{
-                k: v
-                for k, v in sample.items() if k != '__key__'
-            } )
+        # try:
+        #     assert type( sample ) == dict
+        #     return cls.sample_class( **{
+        #         k: v
+        #         for k, v in sample.items() if k != '__key__'
+        #     } )
         
-        except Exception as e:
-            # Sample constructor failed -- revert to default
-            return AnySample(
-                value = sample,
-            )
+        # except Exception as e:
+        #     # Sample constructor failed -- revert to default
+        #     return AnySample(
+        #         value = sample,
+        #     )
 
     def wrap_batch( self, batch: WDSRawBatch ) -> SampleBatch[ST]:
         """Wrap a `batch` of samples into the appropriate dataset-specific type
@@ -449,6 +540,9 @@ def packable( cls ):
     
     ##
 
+    class_name = cls.__name__
+    class_annotations = cls.__annotations__
+
     # Add in dataclass niceness to original class
     as_dataclass = dataclass( cls )
 
@@ -458,8 +552,9 @@ def packable( cls ):
         def __post_init__( self ):
             return PackableSample.__post_init__( self )
     
-    as_packable.__name__ = cls.__name__
-    as_packable.__annotations__ = cls.__annotations__
+    # TODO This doesn't properly carry over the original
+    as_packable.__name__ = class_name
+    as_packable.__annotations__ = class_annotations
 
     ##
 

atdata/lens.py

@@ -0,0 +1,200 @@
+"""Lenses between typed datasets"""
+
+##
+# Imports
+
+import functools
+import inspect
+
+from typing import (
+    TypeAlias,
+    Type,
+    TypeVar,
+    Tuple,
+    Dict,
+    Callable,
+    Optional,
+    Generic,
+    #
+    TYPE_CHECKING
+)
+
+if TYPE_CHECKING:
+    from .dataset import PackableSample
+
+
+##
+# Typing helpers
+
+DatasetType: TypeAlias = Type['PackableSample']
+LensSignature: TypeAlias = Tuple[DatasetType, DatasetType]
+
+S = TypeVar( 'S', bound = 'PackableSample' )
+V = TypeVar( 'V', bound = 'PackableSample' )
+type LensGetter[S, V] = Callable[[S], V]
+type LensPutter[S, V] = Callable[[V, S], S]
+
+
+##
+# Shortcut decorators
+
+class Lens( Generic[S, V] ):
+    """TODO"""
+
+    # @property
+    # def source_type( self ) -> Type[S]:
+    #     """The source type (S) for the lens; what is put to"""
+    #     # TODO Figure out why linting fails here
+    #     return self.__orig_class__.__args__[0]
+
+    # @property
+    # def view_type( self ) -> Type[V]:
+    #     """The view type (V) for the lens; what is get'd from"""
+    #     # TODO FIgure out why linting fails here
+    #     return self.__orig_class__.__args__[1]
+
+    def __init__( self, get: LensGetter[S, V],
+                put: Optional[LensPutter[S, V]] = None
+            ) -> None:
+        """TODO"""
+        ##
+
+        # Check argument validity
+
+        sig = inspect.signature( get )
+        input_types = list( sig.parameters.values() )
+        assert len( input_types ) == 1, \
+            'Wrong number of input args for lens: should only have one'
+
+        # Update function details for this object as returned by annotation
+        functools.update_wrapper( self, get )
+
+        self.source_type: Type[PackableSample] = input_types[0].annotation
+        self.view_type = sig.return_annotation
+
+        # Store the getter
+        self._getter = get
+        
+        # Determine and store the putter
+        if put is None:
+            # Trivial putter does not update the source
+            def _trivial_put( v: V, s: S ) -> S:
+                return s
+            put = _trivial_put
+        self._putter = put
+    
+    #
+
+    def putter( self, put: LensPutter[S, V] ) -> LensPutter[S, V]:
+        """TODO"""
+        ##
+        self._putter = put
+        return put
+    
+    # Methods to actually execute transformations
+
+    def put( self, v: V, s: S ) -> S:
+        """TODO"""
+        return self._putter( v, s )
+
+    def get( self, s: S ) -> V:
+        """TODO"""
+        return self( s )
+
+    # Convenience to enable calling the lens as its getter
+    
+    def __call__( self, s: S ) -> V:
+        return self._getter( s )
+
+# TODO Figure out how to properly parameterize this
+# def _lens_factory[S, V]( register: bool = True ):
+#     """Register the annotated function `f` as the getter of a sample lens"""
+
+#     # The actual lens decorator taking a lens getter function to a lens object
+#     def _decorator( f: LensGetter[S, V] ) -> Lens[S, V]:
+#         ret = Lens[S, V]( f )
+#         if register:
+#             _network.register( ret )
+#         return ret
+    
+#     # Return the lens decorator
+#     return _decorator
+
+# # For convenience
+# lens = _lens_factory
+
+def lens(  f: LensGetter[S, V] ) -> Lens[S, V]:
+    ret = Lens[S, V]( f )
+    _network.register( ret )
+    return ret
+
+
+##
+# Global registry of used lenses
+
+# _registered_lenses: Dict[LensSignature, Lens] = dict()
+# """TODO"""
+
+class LensNetwork:
+    """TODO"""
+
+    _instance = None
+    """The singleton instance"""
+
+    def __new__(cls, *args, **kwargs):
+        if cls._instance is None:
+            # If no instance exists, create a new one
+            cls._instance = super().__new__(cls)
+        return cls._instance  # Return the existing (or newly created) instance
+
+    def __init__(self):
+        if not hasattr(self, '_initialized'):  # Check if already initialized
+            self._registry: Dict[LensSignature, Lens] = dict()
+            self._initialized = True
+    
+    def register( self, _lens: Lens ):
+        """Set `lens` as the canonical view between its source and view types"""
+    
+        # sig = inspect.signature( _lens.get )
+        # input_types = list( sig.parameters.values() )
+        # assert len( input_types ) == 1, \
+        #     'Wrong number of input args for lens: should only have one'
+        
+        # input_type = input_types[0].annotation
+        # print( input_type )
+        # output_type = sig.return_annotation
+
+        # self._registry[input_type, output_type] = _lens
+        print( _lens.source_type )
+        self._registry[_lens.source_type, _lens.view_type] = _lens
+    
+    def transform( self, source: DatasetType, view: DatasetType ) -> Lens:
+        """TODO"""
+
+        # TODO Handle compositional closure
+        ret = self._registry.get( (source, view), None )
+        if ret is None:
+            raise ValueError( f'No registered lens from source {source} to view {view}' )
+        
+        return ret
+
+
+# Create global singleton registry instance
+_network = LensNetwork()
+
+# def lens( f: LensPutter ) -> Lens:
+#     """Register the annotated function `f` as a sample lens"""
+#     ##
+    
+#     sig = inspect.signature( f )
+
+#     input_types = list( sig.parameters.values() )
+#     output_type = sig.return_annotation
+    
+#     _registered_lenses[]
+
+#     f.lens = Lens(
+
+#     )
+
+#     return f

{atdata-0.1.2a4.dist-info → atdata-0.1.3a2.dist-info}/METADATA

@@ -1,13 +1,16 @@
 Metadata-Version: 2.4
 Name: atdata
-Version: 0.1.2a4
+Version: 0.1.3a2
 Summary: A loose federation of distributed, typed datasets
 Author-email: Maxine Levesque <hello@maxine.science>
 License-File: LICENSE
 Requires-Python: >=3.12
+Requires-Dist: fastparquet>=2024.11.0
 Requires-Dist: msgpack>=1.1.2
 Requires-Dist: numpy>=2.3.4
 Requires-Dist: ormsgpack>=1.11.0
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: tqdm>=4.67.1
 Requires-Dist: webdataset>=1.0.2
 Description-Content-Type: text/markdown
 

atdata-0.1.3a2.dist-info/RECORD

@@ -0,0 +1,9 @@
+atdata/__init__.py,sha256=V2qBg7i2mfCNG9nww6Gi_fDp7iwolDMrNzhmNO6VA7M,233
+atdata/_helpers.py,sha256=R63JhXewAKZYnZ9Th7R6yZh0IOUPYGBsth3FpRUMD-U,503
+atdata/dataset.py,sha256=brNKGMkA_au2nLF5oUmjwub1E08DVwBKl9PnzPV6rPM,16722
+atdata/lens.py,sha256=bGlxQ6PEnLj5poQ41DHj1LfpsmI5fELnjnUf4qXOsCo,5304
+atdata-0.1.3a2.dist-info/METADATA,sha256=pYLvssfCzaiqer4yZQM3vh7nRlP8ZcEutXA8po7GZC0,529
+atdata-0.1.3a2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+atdata-0.1.3a2.dist-info/entry_points.txt,sha256=6-iQr1veSTq-ac94bLyfcyGHprrZWevPEd12BWX37tQ,39
+atdata-0.1.3a2.dist-info/licenses/LICENSE,sha256=Pz2eACSxkhsGfW9_iN60pgy-enjnbGTj8df8O3ebnQQ,16726
+atdata-0.1.3a2.dist-info/RECORD,,

atdata-0.1.2a4.dist-info/RECORD

@@ -1,8 +0,0 @@
-atdata/__init__.py,sha256=jPZVd_6UIo0DSbCnXAnYZ2eMwHYzOk--5vtEDTZvwqw,173
-atdata/_helpers.py,sha256=R63JhXewAKZYnZ9Th7R6yZh0IOUPYGBsth3FpRUMD-U,503
-atdata/dataset.py,sha256=4cfxyET8470RGKvHvseH8KZBQvTjevovPr_JGVwj854,13518
-atdata-0.1.2a4.dist-info/METADATA,sha256=igT4Js5SEl5IUhWX6AqDYdROQ022LCx_qfT3PMLifjI,434
-atdata-0.1.2a4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-atdata-0.1.2a4.dist-info/entry_points.txt,sha256=6-iQr1veSTq-ac94bLyfcyGHprrZWevPEd12BWX37tQ,39
-atdata-0.1.2a4.dist-info/licenses/LICENSE,sha256=Pz2eACSxkhsGfW9_iN60pgy-enjnbGTj8df8O3ebnQQ,16726
-atdata-0.1.2a4.dist-info/RECORD,,