fix mypy errors

dacapo/blockwise/argmax_worker.py

@@ -3,6 +3,7 @@
 
 from dacapo.store.array_store import LocalArrayIdentifier
 from dacapo.compute_context import create_compute_context
+from dacapo.tmp import open_from_identifier
 
 import daisy
 

dacapo/blockwise/segment_worker.py

@@ -10,6 +10,7 @@
 import numpy as np
 import yaml
 from dacapo.compute_context import create_compute_context
+from dacapo.tmp import open_from_identifier
 
 
 from dacapo.store.array_store import LocalArrayIdentifier

dacapo/blockwise/threshold_worker.py

@@ -3,6 +3,7 @@
 
 from dacapo.store.array_store import LocalArrayIdentifier
 from dacapo.compute_context import create_compute_context
+from dacapo.tmp import open_from_identifier
 
 import daisy
 

dacapo/experiments/datasplits/datasets/arrays/concat_array_config.py

@@ -43,7 +43,7 @@ class ConcatArrayConfig(ArrayConfig):
     )
 
     def array(self, mode: str = "r") -> Array:
-        arrays = [config.array(mode) for _, config in self.source_array_configs]
+        arrays = [config.array(mode) for _, config in self.source_array_configs.items()]
 
         out_array = Array(
             da.zeros(len(arrays), *arrays[0].physical_shape, dtype=arrays[0].dtype),

dacapo/experiments/datasplits/datasets/arrays/crop_array_config.py

@@ -37,7 +37,7 @@ class CropArrayConfig(ArrayConfig):
 
     def array(self, mode: str = "r") -> Array:
         source_array = self.source_array_config.array(mode)
-        roi_slices = source_array._Array__slices(self.roi)
+        roi_slices = getattr(source_array, "_Array__slices")(self.roi)
         out_array = Array(
             source_array.data[roi_slices],
             self.roi.offset,

dacapo/experiments/datasplits/datasets/arrays/dvid_array_config.py

@@ -31,6 +31,7 @@ def array(self, mode: str = "r") -> Array:
         # To handle this case we would need to subclass `funlib.persistence.Array` to
         # directly read from DVID
         raise NotImplementedError("NotImplemented")
+        """
         from dacapo.ext import NoSuchModule
 
         try:
@@ -47,6 +48,7 @@ def array(self, mode: str = "r") -> Array:
         )
         dtype = np.dtype(self.attrs["Extended"]["Values"][0]["DataType"])
         raise NotImplementedError
+        """
 
     def verify(self) -> Tuple[bool, str]:
         """

dacapo/experiments/datasplits/datasets/arrays/missing_annotations_mask_config.py

@@ -41,17 +41,17 @@ class MissingAnnotationsMaskConfig(ArrayConfig):
 
     def array(self, mode: str = "r") -> Array:
         labels = self.source_array_config.array(mode)
-        grouped = da.ones((len(self._groupings), *labels.shape), dtype=bool)
-        grouped[:] = labels > 0
-        labels_list = LabelList.parse_obj({"labels": self.attrs["labels"]}).labels
+        grouped = da.ones((len(self.groupings), *labels.shape), dtype=bool)
+        grouped[:] = labels.data > 0
+        labels_list = LabelList.parse_obj({"labels": labels._source_data.attrs["labels"]}).labels
         present_not_annotated = set(
             [
                 label.value
                 for label in labels_list
                 if label.annotationState.present and not label.annotationState.annotated
             ]
         )
-        for i, (_, ids) in enumerate(self._groupings):
+        for i, (_, ids) in enumerate(self.groupings):
             if any([id in present_not_annotated for id in ids]):
                 grouped[i] = 0
 

dacapo/experiments/datasplits/datasets/arrays/tiff_array_config.py

@@ -48,7 +48,7 @@ class TiffArrayConfig(ArrayConfig):
     def array(self, mode: str = "r") -> Array:
 
         return Array(
-            data=tifffile.TiffFile(self._file_name).values,
+            data=tifffile.TiffFile(self.file_name).values,
             offset=self.offset,
             voxel_size=self.voxel_size,
             axis_names=self.axis_names,

dacapo/experiments/datasplits/datasplit_generator.py

@@ -1,4 +1,5 @@
 from dacapo.experiments.tasks import TaskConfig
+from dacapo.experiments.datasplits.datasets.arrays import ArrayConfig
 from upath import UPath as Path
 from typing import List, Union, Optional, Sequence
 from enum import Enum, EnumMeta

dacapo/experiments/tasks/evaluators/evaluator.py

@@ -4,11 +4,11 @@
 from typing import Tuple, Dict, Optional, List, TYPE_CHECKING, Union
 import math
 import itertools
+from funlib.persistence import Array
 
 if TYPE_CHECKING:
     from dacapo.experiments.tasks.evaluators.evaluation_scores import EvaluationScores
     from dacapo.experiments.datasplits.datasets import Dataset
-    from dacapo.experiments.datasplits.datasets.arrays import Array
     from dacapo.store.local_array_store import LocalArrayIdentifier
     from dacapo.experiments.tasks.post_processors import PostProcessorParameters
     from dacapo.experiments.validation_scores import ValidationScores
@@ -57,7 +57,7 @@ class Evaluator(ABC):
 
     @abstractmethod
     def evaluate(
-        self, output_array_identifier: "LocalArrayIdentifier", evaluation_array: "Array"
+        self, output_array_identifier: "LocalArrayIdentifier", evaluation_array: Array
     ) -> "EvaluationScores":
         """
         Compares and evaluates the output array against the evaluation array.

dacapo/experiments/tasks/post_processors/post_processor.py

@@ -1,13 +1,13 @@
 from abc import ABC, abstractmethod
 from funlib.geometry import Coordinate
+from funlib.persistence import Array
 
 from typing import Iterable, TYPE_CHECKING
 
 if TYPE_CHECKING:
     from dacapo.experiments.tasks.post_processors.post_processor_parameters import (
         PostProcessorParameters,
     )
-    from dacapo.experiments.datasplits.datasets.arrays import Array
     from dacapo.store.local_array_store import LocalArrayIdentifier
 
 
@@ -86,7 +86,7 @@ def process(
         output_array_identifier: "LocalArrayIdentifier",
         num_workers: int = 16,
         chunk_size: Coordinate = Coordinate((64, 64, 64)),
-    ) -> "Array":
+    ) -> Array:
         """
         Convert predictions into the final output.
 

dacapo/experiments/tasks/predictors/predictor.py

@@ -1,12 +1,12 @@
 from funlib.geometry import Coordinate
+from funlib.persistence import Array
 
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING, Any, Tuple
 
 if TYPE_CHECKING:
     from dacapo.experiments.architectures.architecture import Architecture
     from dacapo.experiments.model import Model
-    from dacapo.experiments.datasplits.datasets.arrays import Array
 
 
 class Predictor(ABC):
@@ -19,8 +19,8 @@ class Predictor(ABC):
 
     Methods:
         create_model(self, architecture: "Architecture") -> "Model": Given a training architecture, create a model for this predictor.
-        create_target(self, gt: "Array") -> "Array": Create the target array for training, given a ground-truth array.
-        create_weight(self, gt: "Array", target: "Array", mask: "Array", moving_class_counts: Any) -> Tuple["Array", Any]: Create the weight array for training, given a ground-truth and associated target array.
+        create_target(self, gt: Array) -> Array: Create the target array for training, given a ground-truth array.
+        create_weight(self, gt: Array, target: Array, mask: Array, moving_class_counts: Any) -> Tuple[Array, Any]: Create the weight array for training, given a ground-truth and associated target array.
         gt_region_for_roi(self, target_spec): Report how much spatial context this predictor needs to generate a target for the given ROI.
         padding(self, gt_voxel_size: Coordinate) -> Coordinate: Return the padding needed for the ground-truth array.
     Notes:
@@ -48,7 +48,7 @@ def create_model(self, architecture: "Architecture") -> "Model":
         pass
 
     @abstractmethod
-    def create_target(self, gt: "Array") -> "Array":
+    def create_target(self, gt: Array) -> Array:
         """
         Create the target array for training, given a ground-truth array.
 
@@ -83,11 +83,11 @@ def create_target(self, gt: "Array") -> "Array":
     @abstractmethod
     def create_weight(
         self,
-        gt: "Array",
-        target: "Array",
-        mask: "Array",
+        gt: Array,
+        target: Array,
+        mask: Array,
         moving_class_counts: Any,
-    ) -> Tuple["Array", Any]:
+    ) -> Tuple[Array, Any]:
         """
         Create the weight array for training, given a ground-truth and
         associated target array.

dacapo/predict.py

@@ -129,10 +129,15 @@ def predict(
         axis_names = ["c^"] + raw_array.axis_names
     else:
         axis_names = raw_array.axis_names
+
+    if isinstance(output_roi, Roi):
+        out_roi: Roi = output_roi
+    else:
+        raise ValueError("out_roi must be a roi")
     create_from_identifier(
         output_array_identifier,
         axis_names,
-        output_roi,
+        out_roi,
         num_out_channels,
         output_voxel_size,
         output_dtype,

dacapo/tmp.py

@@ -67,16 +67,16 @@ def create_from_identifier(
     if not out_path.parent.exists():
         out_path.parent.mkdir(parents=True)
 
-    num_channels = [num_channels] if num_channels is not None else []
+    list_num_channels = [num_channels] if num_channels is not None else []
     return prepare_ds(
         out_path,
-        shape=(*num_channels, *roi.shape / voxel_size),
+        shape=(*list_num_channels, *roi.shape / voxel_size),
         offset=roi.offset / voxel_size,
         voxel_size=voxel_size,
         axis_names=axis_names,
         dtype=dtype,
         chunk_shape=(
-            (*num_channels, *write_size / voxel_size)
+            (*list_num_channels, *write_size / voxel_size)
             if write_size is not None
             else None
         ),