BDP Tools (#88)

Add reconstruction data prep utility to facilitate beamline data pipeline integration

ptychodus/__main__.py

@@ -4,7 +4,7 @@
 import argparse
 import sys
 
-from ptychodus.model import ModelArgs, ModelCore
+from ptychodus.model import ModelCore
 import ptychodus
 
 
@@ -17,17 +17,6 @@ def verifyAllArgumentsParsed(parser: argparse.ArgumentParser, argv: list[str]) -
         parser.error('unrecognized arguments: %s' % ' '.join(argv))
 
 
-class DirectoryType:
-
-    def __call__(self, string: str) -> Path:
-        path = Path(string)
-
-        if not path.is_dir():
-            raise argparse.ArgumentTypeError(f'\"{string}\" is not a directory!')
-
-        return path
-
-
 def main() -> int:
     parser = argparse.ArgumentParser(
         prog=ptychodus.__name__.lower(),
@@ -46,25 +35,18 @@ def main() -> int:
         help=argparse.SUPPRESS,
     )
     parser.add_argument(
-        '-f',
-        '--file-prefix',
-        help='replace file path prefix in settings',
-    )
-    parser.add_argument(
-        # input data product file (batch mode)
         '-i',
         '--input',
         metavar='INPUT_FILE',
         type=argparse.FileType('r'),
-        help=argparse.SUPPRESS,
+        help='input file (batch mode)',
     )
     parser.add_argument(
-        # output data product file (batch mode)
         '-o',
         '--output',
         metavar='OUTPUT_FILE',
         type=argparse.FileType('w'),
-        help=argparse.SUPPRESS,
+        help='output file (batch mode)',
     )
     parser.add_argument(
         # preprocessed diffraction patterns file (batch mode)
@@ -87,25 +69,14 @@ def main() -> int:
         action='version',
         version=versionString(),
     )
-    parser.add_argument(
-        '-w',
-        '--write',
-        metavar='OUTPUT_DIR',
-        type=DirectoryType(),
-        help='stage reconstruction inputs to directory',
-    )
 
     parsedArgs, unparsedArgs = parser.parse_known_args()
+    settingsFile = Path(parsedArgs.settings.name) if parsedArgs.settings else None
 
-    modelArgs = ModelArgs(
-        settingsFile=Path(parsedArgs.settings.name) if parsedArgs.settings else None,
-        patternsFile=Path(parsedArgs.patterns.name) if parsedArgs.patterns else None,
-        replacementPathPrefix=parsedArgs.file_prefix,
-    )
-
-    with ModelCore(modelArgs, isDeveloperModeEnabled=parsedArgs.dev) as model:
-        if parsedArgs.write is not None:
-            return model.stageReconstructionInputs(parsedArgs.write)
+    with ModelCore(settingsFile, isDeveloperModeEnabled=parsedArgs.dev) as model:
+        if parsedArgs.patterns is not None:
+            patternsFilePath = Path(parsedArgs.patterns.name)
+            model.workflowAPI.importProcessedPatterns(patternsFilePath)
 
         if parsedArgs.batch is not None:
             verifyAllArgumentsParsed(parser, unparsedArgs)
@@ -114,16 +85,10 @@ def main() -> int:
                 parser.error('Batch mode requires input and output arguments!')
                 return -1
 
-            inputPath = Path(parsedArgs.input.name)
-            outputPath = Path(parsedArgs.output.name)
-
-            if parsedArgs.batch == 'reconstruct':
-                return model.batchModeReconstruct(inputPath, outputPath)
-            elif parsedArgs.batch == 'train':
-                return model.batchModeTrain(inputPath, outputPath)
-            else:
-                parser.error(f'Unknown batch mode action \"{parsedArgs.batch}\"!')
-                return -1
+            action = parsedArgs.batch
+            inputFilePath = Path(parsedArgs.input.name)
+            outputFilePath = Path(parsedArgs.output.name)
+            return model.batchModeExecute(action, inputFilePath, outputFilePath)
 
         try:
             from PyQt5.QtWidgets import QApplication

ptychodus/api/plugins.py

@@ -8,7 +8,6 @@
 import pkgutil
 import re
 
-from .automation import FileBasedWorkflow
 from .fluorescence import (DeconvolutionStrategy, FluorescenceFileReader, FluorescenceFileWriter,
                            UpscalingStrategy)
 from .object import ObjectPhaseCenteringStrategy, ObjectFileReader, ObjectFileWriter
@@ -17,6 +16,7 @@
 from .probe import FresnelZonePlate, ProbeFileReader, ProbeFileWriter
 from .product import ProductFileReader, ProductFileWriter
 from .scan import ScanFileReader, ScanFileWriter
+from .workflow import FileBasedWorkflow
 
 __all__ = [
     'PluginChooser',

ptychodus/api/settings.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 from collections.abc import Iterator, Sequence
+from dataclasses import dataclass
 from decimal import Decimal
 from pathlib import Path
-from typing import Any, Callable, Final, Generic, TypeVar
+from typing import Any, Callable, Generic, TypeVar
 from uuid import UUID
 import configparser
 import logging
@@ -14,6 +15,12 @@
 logger = logging.getLogger(__name__)
 
 
+@dataclass(frozen=True)
+class PathPrefixChange:
+    findPathPrefix: Path
+    replacementPathPrefix: Path
+
+
 class SettingsEntry(Generic[T], Observable):
 
     def __init__(self, name: str, defaultValue: T, stringConverter: Callable[[str], T]) -> None:
@@ -115,11 +122,9 @@ def update(self, observable: Observable) -> None:
 
 
 class SettingsRegistry(Observable):
-    PREFIX_PLACEHOLDER_TEXT: Final[str] = 'PREFIX'
 
-    def __init__(self, replacementPathPrefix: str | None) -> None:
+    def __init__(self) -> None:
         super().__init__()
-        self._replacementPathPrefix = replacementPathPrefix
         self._groupList: list[SettingsGroup] = list()
         self._fileFilterList: list[str] = ['Initialization Files (*.ini)']
 
@@ -142,12 +147,6 @@ def __getitem__(self, index: int) -> SettingsGroup:
     def __len__(self) -> int:
         return len(self._groupList)
 
-    def getReplacementPathPrefix(self) -> str | None:
-        return self._replacementPathPrefix
-
-    def setReplacementPathPrefix(self, replacementPathPrefix: str) -> None:
-        self._replacementPathPrefix = replacementPathPrefix
-
     def getOpenFileFilterList(self) -> Sequence[str]:
         return self._fileFilterList
 
@@ -166,13 +165,6 @@ def openSettings(self, filePath: Path) -> None:
             for settingsEntry in settingsGroup:
                 if config.has_option(settingsGroup.name, settingsEntry.name):
                     valueString = config.get(settingsGroup.name, settingsEntry.name)
-
-                    if self._replacementPathPrefix is not None \
-                            and isinstance(settingsEntry.value, Path):
-                        if valueString.startswith(SettingsRegistry.PREFIX_PLACEHOLDER_TEXT):
-                            valueString = self._replacementPathPrefix \
-                                    + valueString[len(SettingsRegistry.PREFIX_PLACEHOLDER_TEXT):]
-
                     settingsEntry.setValueFromString(valueString)
 
         self.notifyObservers()
@@ -183,7 +175,9 @@ def getSaveFileFilterList(self) -> Sequence[str]:
     def getSaveFileFilter(self) -> str:
         return self._fileFilterList[0]
 
-    def saveSettings(self, filePath: Path) -> None:
+    def saveSettings(self,
+                     filePath: Path,
+                     changePathPrefix: PathPrefixChange | None = None) -> None:
         config = configparser.ConfigParser(interpolation=None)
         setattr(config, 'optionxform', lambda option: option)
 
@@ -193,10 +187,16 @@ def saveSettings(self, filePath: Path) -> None:
             for settingsEntry in settingsGroup:
                 valueString = str(settingsEntry.value)
 
-                if self._replacementPathPrefix and isinstance(settingsEntry.value, Path):
-                    if valueString.startswith(self._replacementPathPrefix):
-                        valueString = SettingsRegistry.PREFIX_PLACEHOLDER_TEXT \
-                                + valueString[len(self._replacementPathPrefix):]
+                if changePathPrefix and isinstance(settingsEntry.value, Path):
+                    try:
+                        relativePath = settingsEntry.value.relative_to(
+                            changePathPrefix.findPathPrefix)
+                    except ValueError:
+                        pass
+                    else:
+                        modifiedPath = changePathPrefix.replacementPathPrefix / relativePath
+                        valueString = str(modifiedPath)
+
                 config.set(settingsGroup.name, settingsEntry.name, valueString)
 
         logger.debug(f'Writing settings to \"{filePath}\"')

ptychodus/api/workflow.py

@@ -0,0 +1,106 @@
+from abc import ABC, abstractmethod
+from collections.abc import Mapping
+from pathlib import Path
+from typing import Any
+
+from ptychodus.api.geometry import ImageExtent
+from ptychodus.api.patterns import CropCenter
+from ptychodus.api.settings import PathPrefixChange
+
+
+class WorkflowProductAPI(ABC):
+
+    @abstractmethod
+    def openScan(self, filePath: Path, *, fileType: str | None = None) -> None:
+        pass
+
+    @abstractmethod
+    def buildScan(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
+        pass
+
+    @abstractmethod
+    def openProbe(self, filePath: Path, *, fileType: str | None = None) -> None:
+        pass
+
+    @abstractmethod
+    def buildProbe(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
+        pass
+
+    @abstractmethod
+    def openObject(self, filePath: Path, *, fileType: str | None = None) -> None:
+        pass
+
+    @abstractmethod
+    def buildObject(self, builderName: str, builderParameters: Mapping[str, Any] = {}) -> None:
+        pass
+
+    @abstractmethod
+    def reconstruct(self) -> None:
+        pass
+
+    @abstractmethod
+    def saveProduct(self, filePath: Path, *, fileType: str | None = None) -> None:
+        pass
+
+
+class WorkflowAPI(ABC):
+
+    @abstractmethod
+    def openPatterns(
+        self,
+        filePath: Path,
+        *,
+        fileType: str | None = None,
+        cropCenter: CropCenter | None = None,
+        cropExtent: ImageExtent | None = None,
+    ) -> None:
+        '''opens diffraction patterns from file'''
+        pass
+
+    @abstractmethod
+    def importProcessedPatterns(self, filePath: Path) -> None:
+        '''import processed patterns'''
+        pass
+
+    @abstractmethod
+    def exportProcessedPatterns(self, filePath: Path) -> None:
+        '''export processed patterns'''
+        pass
+
+    @abstractmethod
+    def openProduct(self, filePath: Path, *, fileType: str | None = None) -> WorkflowProductAPI:
+        '''opens product from file'''
+        pass
+
+    @abstractmethod
+    def createProduct(
+        self,
+        name: str,
+        *,
+        comments: str = '',
+        detectorDistanceInMeters: float | None = None,
+        probeEnergyInElectronVolts: float | None = None,
+        probePhotonsPerSecond: float | None = None,
+        exposureTimeInSeconds: float | None = None,
+    ) -> WorkflowProductAPI:
+        '''creates a new product'''
+        pass
+
+    @abstractmethod
+    def saveSettings(self,
+                     filePath: Path,
+                     changePathPrefix: PathPrefixChange | None = None) -> None:
+        pass
+
+
+class FileBasedWorkflow(ABC):
+
+    @abstractmethod
+    def getFilePattern(self) -> str:
+        '''UNIX-style filename pattern. For rules see fnmatch from Python standard library.'''
+        pass
+
+    @abstractmethod
+    def execute(self, api: WorkflowAPI, filePath: Path) -> None:
+        '''uses workflow API to execute the workflow'''
+        pass