dummy-spatialdata 0.1.8__tar.gz → 0.1.10__tar.gz

dummy_spatialdata-0.1.10/PKG-INFO

@@ -0,0 +1,134 @@
+Metadata-Version: 2.4
+Name: dummy-spatialdata
+Version: 0.1.10
+Summary: A package for creating arbitrary spatialdata for testing purposes.
+Project-URL: Documentation, https://dummy-spatialdata.readthedocs.io/
+Project-URL: Homepage, https://github.com/BIMSBBioinfo/dummy-spatialdata
+Project-URL: Source, https://github.com/BIMSBBioinfo/dummy-spatialdata
+Author-email: Artür Manukyan <amanukyan.umms@gmail.com>
+License: MIT
+Requires-Python: >=3.12
+Requires-Dist: dummy-anndata>=0.0.3
+Requires-Dist: geopandas
+Requires-Dist: pillow
+Requires-Dist: requests
+Requires-Dist: shapely
+Requires-Dist: spatialdata>=0.5.0
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine>=4.0.2; extra == 'dev'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+# dummy-spatialdata
+
+Allows generating dummy spatialdata objects, which can be useful for testing purposes.
+
+## Installation
+
+```bash
+pip install dummy-spatialdata
+```
+
+## Example usage
+
+`dummy-spatialdata` is compatible with both spatialdata == 0.5.0 (zarr v2) and 0.7.2 (zarr v3)
+
+Thus please use 
+
+1. `conda create --name dummy_sd_env python==3.12 spatialdata==0.7.2` or 
+2. `conda create --name dummy_sd_env_05 python==3.12 spatialdata==0.5.0 setuptools==75.8.0`
+
+```{python}
+from dummy_spatialdata import generate_dataset
+import dummy_anndata
+import spatialdata_plot as sdp 
+import spatialdata as sd
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import anndata as ad
+import tempfile as tf
+
+# generate spatialdata
+sdata = generate_dataset(
+    images = [
+        {'type': 'rgb', 'scale_factors': [2,2,2], 'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+    ],
+    labels = [
+        {'n': 12, 'scale_factors': [2,2,2],  'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+        {'n': 12, 'scale_factors': [2,2,2],  'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+    ],
+    shapes = [
+        {'n': 12, 'type': 'polygon', 'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+        {'n': 12, 'type': 'circle', 'shape': {'x': 64, 'y': 64},
+         'overlapping': False, 'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']}
+    ],
+    points = [
+        {'n': 12, 'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']}
+    ],
+    tables = [
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'shape', 'element_index': 0},
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'shape', 'element_index': 1},
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'label', 'element_index': 0},
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'label', 'element_index': 1},
+    ],
+    coordinate_systems = {
+        'identity': {'transformations': ['identity']},
+        'scale': {'transformations': ['scale']},
+        'mapAxis': {'transformations': ['mapAxis']},
+        'translation': {'transformations': ['translation']},
+        'rotation': {'transformations': ['rotation']},
+        'affine': {'transformations': ['affine']},
+        'sequence': {'transformations': ['scale', 'mapAxis', 'translation', 'rotation', 'affine']}
+    },
+    SEED=13
+)
+sdata
+```
+
+```
+SpatialData object
+├── Images
+│     └── 'image_0': DataTree[cyx] (3, 64, 64), (3, 32, 32), (3, 16, 16), (3, 8, 8)
+├── Labels
+│     ├── 'label_0': DataTree[yx] (64, 64), (32, 32), (16, 16), (8, 8)
+│     └── 'label_1': DataTree[yx] (64, 64), (32, 32), (16, 16), (8, 8)
+├── Points
+│     └── 'point_0': DataFrame with shape: (<Delayed>, 2) (2D points)
+├── Shapes
+│     ├── 'shape_0': GeoDataFrame shape: (12, 1) (2D shapes)
+│     └── 'shape_1': GeoDataFrame shape: (12, 2) (2D shapes)
+└── Tables
+      ├── 'table_0': AnnData (12, 20)
+      ├── 'table_1': AnnData (12, 20)
+      ├── 'table_2': AnnData (12, 20)
+      └── 'table_3': AnnData (12, 20)
+with coordinate systems:
+    ▸ 'affine', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'identity', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'mapAxis', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'rotation', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+...
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'sequence', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'translation', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+```
+
+You can plot the demo data now!
+
+```{python}
+sdata.pl.render_images('image_0').pl.render_shapes('shape_0', color='Gene001', table_name = 'table_0', table_layer = 'float_matrix').pl.show(coordinate_systems = 'affine')
+```

dummy_spatialdata-0.1.10/README.md

@@ -0,0 +1,110 @@
+# dummy-spatialdata
+
+Allows generating dummy spatialdata objects, which can be useful for testing purposes.
+
+## Installation
+
+```bash
+pip install dummy-spatialdata
+```
+
+## Example usage
+
+`dummy-spatialdata` is compatible with both spatialdata == 0.5.0 (zarr v2) and 0.7.2 (zarr v3)
+
+Thus please use 
+
+1. `conda create --name dummy_sd_env python==3.12 spatialdata==0.7.2` or 
+2. `conda create --name dummy_sd_env_05 python==3.12 spatialdata==0.5.0 setuptools==75.8.0`
+
+```{python}
+from dummy_spatialdata import generate_dataset
+import dummy_anndata
+import spatialdata_plot as sdp 
+import spatialdata as sd
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import anndata as ad
+import tempfile as tf
+
+# generate spatialdata
+sdata = generate_dataset(
+    images = [
+        {'type': 'rgb', 'scale_factors': [2,2,2], 'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+    ],
+    labels = [
+        {'n': 12, 'scale_factors': [2,2,2],  'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+        {'n': 12, 'scale_factors': [2,2,2],  'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+    ],
+    shapes = [
+        {'n': 12, 'type': 'polygon', 'shape': {'x': 64, 'y': 64},
+         'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']},
+        {'n': 12, 'type': 'circle', 'shape': {'x': 64, 'y': 64},
+         'overlapping': False, 'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']}
+    ],
+    points = [
+        {'n': 12, 'coordinate_system': ['identity', 'scale', 'mapAxis', 'translation', 'rotation', 'affine', 'sequence']}
+    ],
+    tables = [
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'shape', 'element_index': 0},
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'shape', 'element_index': 1},
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'label', 'element_index': 0},
+        {'table': dummy_anndata.generate_dataset(n_obs=12, n_vars=20), 'element': 'label', 'element_index': 1},
+    ],
+    coordinate_systems = {
+        'identity': {'transformations': ['identity']},
+        'scale': {'transformations': ['scale']},
+        'mapAxis': {'transformations': ['mapAxis']},
+        'translation': {'transformations': ['translation']},
+        'rotation': {'transformations': ['rotation']},
+        'affine': {'transformations': ['affine']},
+        'sequence': {'transformations': ['scale', 'mapAxis', 'translation', 'rotation', 'affine']}
+    },
+    SEED=13
+)
+sdata
+```
+
+```
+SpatialData object
+├── Images
+│     └── 'image_0': DataTree[cyx] (3, 64, 64), (3, 32, 32), (3, 16, 16), (3, 8, 8)
+├── Labels
+│     ├── 'label_0': DataTree[yx] (64, 64), (32, 32), (16, 16), (8, 8)
+│     └── 'label_1': DataTree[yx] (64, 64), (32, 32), (16, 16), (8, 8)
+├── Points
+│     └── 'point_0': DataFrame with shape: (<Delayed>, 2) (2D points)
+├── Shapes
+│     ├── 'shape_0': GeoDataFrame shape: (12, 1) (2D shapes)
+│     └── 'shape_1': GeoDataFrame shape: (12, 2) (2D shapes)
+└── Tables
+      ├── 'table_0': AnnData (12, 20)
+      ├── 'table_1': AnnData (12, 20)
+      ├── 'table_2': AnnData (12, 20)
+      └── 'table_3': AnnData (12, 20)
+with coordinate systems:
+    ▸ 'affine', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'identity', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'mapAxis', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'rotation', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+...
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'sequence', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+    ▸ 'translation', with elements:
+        image_0 (Images), label_0 (Labels), label_1 (Labels), point_0 (Points), shape_0 (Shapes), shape_1 (Shapes)
+```
+
+You can plot the demo data now!
+
+```{python}
+sdata.pl.render_images('image_0').pl.render_shapes('shape_0', color='Gene001', table_name = 'table_0', table_layer = 'float_matrix').pl.show(coordinate_systems = 'affine')
+```

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "dummy-spatialdata"
-version = "0.1.8"
+version = "0.1.10"
 description = "A package for creating arbitrary spatialdata for testing purposes."
 readme = "README.md"
 requires-python = ">=3.12"

dummy_spatialdata-0.1.10/src/dummy_spatialdata/.gitignore

@@ -0,0 +1 @@
+__pycache__

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/__init__.py

@@ -5,7 +5,7 @@ from .generate_imagemodel import generate_imagemodel
 from .generate_labelmodel import generate_labelmodel
 from .generate_shapemodel import generate_shapemodel
 from .generate_pointmodel import generate_pointmodel
-from .generate_tablemodel import generate_tablemodel
+from .generate_tablemodel import generate_tablemodel, generate_anndata
 from .generate_transformations import (
     generate_transformations,
     get_basetransformations,
@@ -18,9 +18,10 @@ __all__ = [
     "generate_imagemodel",
     "generate_labelmodel",
     "generate_shapemodel",
-    "generate_pointmodel"
+    "generate_pointmodel",
     "generate_tablemodel",
     "generate_transformations",
+    "generate_anndata",
     "utils"
 ]
 

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_dataset.py

@@ -14,6 +14,9 @@ from .generate_pointmodel import generate_pointmodel
 from .generate_tablemodel import generate_tablemodel    
 from .generate_transformations import generate_transformations
 from spatialdata.models import TableModel
+from spatialdata import get_element_instances
+
+from pandas import RangeIndex
 
 def generate_dataset(
     images: Optional[list] = None,
@@ -141,6 +144,11 @@ def generate_dataset(
             instance_key = tbl.uns['spatialdata_attrs']['instance_key']
             if region in sdata._shared_keys:
                 element = getattr(sdata, element_type + 's')[region]
-                tbl.obs['instance_id'] = element.index    
+                if element_type == 'shape':
+                    tbl.obs['instance_id'] = element.index    
+                elif element_type == 'label':
+                    tbl.obs['instance_id'] = get_element_instances(element)
+                else:
+                    raise ValueError(f"Invalid element type {element_type} in region {region}. Must be either 'shape' or 'label'.")    
 
     return sdata

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_imagemodel.py

@@ -6,10 +6,11 @@ from pathlib import Path
 from importlib.resources import files, as_file
 from PIL import Image
 from typing import Optional
-from spatialdata.models import Image2DModel
+from spatialdata.models import Image2DModel, Image3DModel
 from spatialdata.transformations import set_transformation, Identity
 from .generate_transformations import generate_transformations, get_basetransformations, get_shape
 from .utils import default_shape
+import zarr
 
 def generate_imagemodel(
     input: Optional[dict] = None,
@@ -46,12 +47,12 @@ def generate_imagemodel(
     # check input
     if input is None:
         return None
-    
-    # get shape
-    input.update(
-        {'shape': get_shape(coordinate_systems, 
-                            input['coordinate_system'] if 'coordinate_system' in input else None)}
-    )
+    if 'shape' not in input:
+        input.update({'shape': default_shape()})
+    if 'scale_factors' not in input:
+        input["scale_factors"] = []
+    if 'dim' not in input:
+        input["dim"] = "2d"
 
     # get source 
     resource = files('dummy_spatialdata')
@@ -71,25 +72,35 @@ def generate_imagemodel(
         img = img.reshape(1, *img.shape)
     else:
         raise ValueError('Please type either \'rgb\' or \'grayscale\' for the image type.')   
-    
+
     # get transformations
     coord_systems = get_basetransformations(coordinate_systems)
     if 'coordinate_system' in input:
         coord_system = input['coordinate_system']
-        if coord_system in coord_systems:
-            trans = {coord_system: coord_systems[coord_system]}
-        else: 
-            trans = {key: Identity()}
+        trans = {}
+        for crd in coord_system:
+            if crd in coord_systems:
+                # trans = {crd: coord_systems[crd]}
+                trans.update({crd: coord_systems[crd]})
+            else: 
+                trans = {key: Identity()}
     else:
         trans = {key: Identity()}
 
-    # image model
-    if 'scale_factors' not in input:
-        input["scale_factors"] = []
-    imagemodel = Image2DModel.parse(data=img, 
-                                    scale_factors=input['scale_factors'],
-                                    transformations = trans)
-
+    # de
+    if "z" not in input["shape"]:
+        imagemodel = Image2DModel.parse(data=img, 
+                                        scale_factors=input['scale_factors'],
+                                        transformations = trans)
+    else: 
+        depth = input['shape'].get('z', 2)
+        img = np.stack([img] * depth, axis=-1)
+        img = img.transpose((0, 3, 1, 2))
+        imagemodel = Image3DModel.parse(data=img, 
+                                        dims = ['c', 'z', 'y', 'x'],
+                                        scale_factors=input['scale_factors'],
+                                        transformations = trans)
+    
     return imagemodel
 
 def resize_image(image: Image, input: dict) -> Image:

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_labelmodel.py

@@ -4,7 +4,7 @@ import numpy as np
 
 from importlib.resources import files, as_file
 from typing import Optional
-from spatialdata.models import Labels2DModel
+from spatialdata.models import Labels2DModel, Labels3DModel
 from spatialdata.transformations import set_transformation, Identity
 from .generate_transformations import generate_transformations, get_basetransformations, get_shape
 from .utils import default_shape
@@ -44,12 +44,12 @@ def generate_labelmodel(
     # return None if no input is provided
     if input is None:
         return None
-    
-    # get shape
-    input.update(
-        {'shape': get_shape(coordinate_systems, 
-                            input['coordinate_system'] if 'coordinate_system' in input else None)}
-    )
+    if 'shape' not in input:
+        input.update({'shape': default_shape()})
+    if 'scale_factors' not in input:
+        input["scale_factors"] = []
+    if 'dim' not in input:
+        input["dim"] = "2d"
 
     # generate labels
     # mask for where values should be non-zero
@@ -58,25 +58,35 @@ def generate_labelmodel(
 
     arr = np.zeros((rows, cols), dtype=int)
     mask = np.random.rand(rows, cols) < prob_nonzero
-    arr[mask] = np.random.randint(1, input['n'], size=mask.sum())
-
+    arr[mask] = np.random.randint(1, input['n']+1, size=mask.sum())
+    
     # get transformations
     coord_systems = get_basetransformations(coordinate_systems)
     if 'coordinate_system' in input:
         coord_system = input['coordinate_system']
-        if coord_system in coord_systems:
-            trans = {coord_system: coord_systems[coord_system]}
-        else: 
-            trans = {key: Identity()}
+        trans = {}
+        for crd in coord_system:
+            if crd in coord_systems:
+                # trans = {crd: coord_systems[crd]}
+                trans.update({crd: coord_systems[crd]})
+            else: 
+                trans = {key: Identity()}
     else:
         trans = {key: Identity()}
 
-    # image model
-    if 'scale_factors' not in input:
-        input["scale_factors"] = []
-    labelmodel = Labels2DModel.parse(data=arr, 
-                                     scale_factors=input['scale_factors'],
-                                     transformations = trans)
+    # define model
+    if "z" not in input["shape"]:   
+        labelmodel = Labels2DModel.parse(data=arr, 
+                                         scale_factors=input['scale_factors'],
+                                         transformations = trans)
+    else:   
+        depth = input['shape'].get('z', 2)
+        arr = np.stack([arr] * depth, axis=-1)
+        arr = arr.transpose((2, 0, 1))
+        labelmodel = Labels3DModel.parse(data=arr, 
+                                         dims = ['z', 'y', 'x'],
+                                         scale_factors=input['scale_factors'],
+                                         transformations = trans)
         
     return labelmodel
     

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_pointmodel.py

@@ -47,10 +47,8 @@ def generate_pointmodel(
         return None
 
     # get shape
-    input.update(
-        {'shape': get_shape(coordinate_systems, 
-                            input['coordinate_system'] if 'coordinate_system' in input else None)}
-    )
+    if 'shape' not in input:
+        input.update({'shape': default_shape()})
 
     # generate points
     RADIUS = 0.08 * min(input['shape']['x'], input['shape']['y'])
@@ -62,10 +60,13 @@ def generate_pointmodel(
     coord_systems = get_basetransformations(coordinate_systems)
     if 'coordinate_system' in input:
         coord_system = input['coordinate_system']
-        if coord_system in coord_systems:
-            trans = {coord_system: coord_systems[coord_system]}
-        else: 
-            trans = {key: Identity()}
+        trans = {}
+        for crd in coord_system:
+            if crd in coord_systems:
+                # trans = {crd: coord_systems[crd]}
+                trans.update({crd: coord_systems[crd]})
+            else: 
+                trans = {key: Identity()}
     else:
         trans = {key: Identity()}
 

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_shapemodel.py

@@ -48,16 +48,21 @@ def generate_shapemodel(
         return None
 
     # get shape
-    input.update(
-        {'shape': get_shape(coordinate_systems, 
-                            input['coordinate_system'] if 'coordinate_system' in input else None)}
-    )
+    if 'shape' not in input:
+        input.update({'shape': default_shape()})
 
     # generate polygons
     RADIUS = 0.08 * min(input['shape']['x'], input['shape']['y'])
     MIN_GAP = 0.01 * min(input['shape']['x'], input['shape']['y'])
 
-    centers = generate_non_overlapping_centers(input['shape']['x'], input['shape']['y'], RADIUS, input['n'], MIN_GAP, SEED)
+    if 'overlapping' not in input:
+        input['overlapping'] = True
+    if input['overlapping']:
+        centers = generate_regular_centers(input['shape']['x'], input['shape']['y'], RADIUS, input['n'], SEED)
+    else:
+        centers = generate_non_overlapping_centers(input['shape']['x'], input['shape']['y'], RADIUS, input['n'], min_gap=MIN_GAP, SEED=SEED)
+    # centers = generate_non_overlapping_centers(input['shape']['x'], input['shape']['y'], RADIUS, input['n'], MIN_GAP, SEED)
+    # centers = generate_regular_centers(input['shape']['x'], input['shape']['y'], RADIUS, input['n'], SEED)
     if input['type'] == 'polygon':
         polygon_seeds = [SEED + i for i in range(input['n'])]
         polygons = [Polygon(border_polygon_points(c, RADIUS, 10, SEED = seed)) for c, seed in zip(centers, polygon_seeds)]
@@ -73,10 +78,12 @@ def generate_shapemodel(
     coord_systems = get_basetransformations(coordinate_systems)
     if 'coordinate_system' in input:
         coord_system = input['coordinate_system']
-        if coord_system in coord_systems:
-            trans = {coord_system: coord_systems[coord_system]}
-        else: 
-            trans = {key: Identity()}
+        trans = {}
+        for crd in coord_system:
+            if crd in coord_systems:
+                trans.update({crd: coord_systems[crd]})
+            else: 
+                trans = {key: Identity()}
     else:
         trans = {key: Identity()}
 
@@ -109,6 +116,19 @@ def generate_non_overlapping_centers(width, height, radius, n_circles, min_gap=0
 
     return np.array(centers)
 
+def generate_regular_centers(width, height, radius, n_circles, SEED=1):
+    centers = []
+    tries = 0
+    rng = np.random.default_rng(SEED)
+
+    for _ in range(n_circles):
+        x = rng.uniform(radius, width - radius)
+        y = rng.uniform(radius, height - radius)
+        candidate = (x, y)
+        centers.append(candidate)
+
+    return np.array(centers)
+
 def border_polygon_points(center, radius, n_points, SEED=1):
     cx, cy = center
     rng = np.random.default_rng(SEED)

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_tablemodel.py

@@ -10,6 +10,9 @@ from spatialdata.models import TableModel
 import spatialdata as sd
 from .utils import default_shape
 
+import anndata as ad
+import pandas as pd
+
 def generate_tablemodel(
     input: Optional[dict] = None
 ) -> TableModel:
@@ -44,4 +47,12 @@ def generate_tablemodel(
         'instance_key': 'instance_id',
     }
 
-    return TableModel.parse(input['table'])
+    return TableModel.parse(input['table'])
+
+# generate anndata
+def generate_anndata(n_obs=12, n_vars=20):
+    obs = pd.DataFrame(index=[f'obs_{i}' for i in range(n_obs)])
+    var = pd.DataFrame(index=[f'var_{i}' for i in range(n_vars)])
+    X = np.random.rand(n_obs, n_vars)
+    adata = ad.AnnData(X=X, obs=obs, var=var)
+    return adata

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/src/dummy_spatialdata/generate_transformations.py

@@ -59,9 +59,9 @@ def generate_transformations(
         elif tr == 'mapAxis':
             tr = MapAxis({"x": "y", "y": "x"})
         elif tr == 'translation':
-            tr = Translation([10, 20], axes = ('x', 'y'))
+            tr = Translation([10, -20], axes = ('x', 'y'))
         elif tr == 'scale':
-            tr = Scale([0.5, 0.5], axes = ('x', 'y'))
+            tr = Scale([0.3, 1.3], axes = ('x', 'y'))
         elif tr == 'rotation':
             theta = np.deg2rad(15)
             c = np.cos(theta)

dummy_spatialdata-0.1.10/tests/.gitignore

@@ -0,0 +1 @@
+__pycache__

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/tests/test_basic.py

@@ -25,4 +25,5 @@ def test_generating_singleelement():
     dummy.write(filename.name + '.zarr')
 
     # read back
-    sdata = sd.read_zarr(filename.name + '.zarr')
+    sdata = sd.read_zarr(filename.name + '.zarr')
+    

{dummy_spatialdata-0.1.8 → dummy_spatialdata-0.1.10}/tests/test_models.py

@@ -26,29 +26,29 @@ from spatialdata.transformations import (
 def test_shapemodel():
 
     # returns GeoDataFrame (circle)
-    shp = generate_shapemodel({'n': 12, 'type': 'circle', 'coordinate_system': 'global'}, 'image')
+    shp = generate_shapemodel({'n': 12, 'type': 'circle', 'coordinate_system': ['global']}, 'shape')
     assert isinstance(shp, gpd.GeoDataFrame)
 
     # returns GeoDataFrame (polygon)
-    shp = generate_shapemodel({'n': 12, 'type': 'polygon', 'coordinate_system': 'global'}, 'image')
+    shp = generate_shapemodel({'n': 12, 'type': 'polygon', 'coordinate_system': ['global']}, 'shape')
     assert isinstance(shp, gpd.GeoDataFrame)
 
     # wrong shape type
     with pytest.raises(ValueError):
-        shp = generate_shapemodel({'n': 12, 'type': 'art', 'coordinate_system': 'global'}, 'image')
+        shp = generate_shapemodel({'n': 12, 'type': 'art', 'coordinate_system': ['global']}, 'shape')
 
     # size is not defined
     with pytest.raises(KeyError):
-        shp = generate_shapemodel({'type': 'circle', 'coordinate_system': 'global'}, 'image')
+        shp = generate_shapemodel({'type': 'circle', 'coordinate_system': ['global']}, 'shape')
 
     # no coordinate system returns element name as coord system and Identity transformation
-    shp = generate_shapemodel({'n': 12, 'type': 'circle'}, 'image')
-    assert list(shp.attrs['transform'].keys())[0] == 'image'
-    assert get_transformation(shp, 'image') == Identity()
+    shp = generate_shapemodel({'n': 12, 'type': 'circle'}, 'shape')
+    assert list(shp.attrs['transform'].keys())[0] == 'shape'
+    assert get_transformation(shp, 'shape') == Identity()
     
     # parses coordinate system
     coord_system = {'global': {'transformations': ['affine'], 'shape': {'x': 2000, 'y': 2000}}}
-    shp = generate_shapemodel({'n': 12, 'type': 'polygon', 'coordinate_system': 'global'}, 'image', coord_system)
+    shp = generate_shapemodel({'n': 12, 'type': 'polygon', 'coordinate_system': ['global']}, 'image', coord_system)
     assert len(list(shp.attrs['transform'].keys())) == 1
     assert list(shp.attrs['transform'].keys())[0] == 'global'
     assert isinstance(get_transformation(shp, 'global'), Affine)
@@ -60,12 +60,12 @@ def test_shapemodel():
 def test_pointmodel():
 
     # returns DataFrame
-    pts = generate_pointmodel({'n': 12, 'coordinate_system': 'global'}, 'image')
+    pts = generate_pointmodel({'n': 12, 'coordinate_system': ['global']}, 'image')
     assert isinstance(pts, dd.DataFrame)
 
     # size is not defined
     with pytest.raises(KeyError):
-        pts = generate_pointmodel({'coordinate_system': 'global'}, 'image')
+        pts = generate_pointmodel({'coordinate_system': ['global']}, 'image')
 
     # no coordinate system returns element name as coord system and Identity transformation
     pts = generate_pointmodel({'n': 12}, 'image')
@@ -74,7 +74,7 @@ def test_pointmodel():
 
     # parses coordinate system
     coord_system = {'global': {'transformations': ['affine'], 'shape': {'x': 2000, 'y': 2000}}}
-    pts = generate_pointmodel({'n': 12, 'coordinate_system': 'global'}, 'image', coord_system)
+    pts = generate_pointmodel({'n': 12, 'coordinate_system': ['global']}, 'image', coord_system)
     assert len(list(pts.attrs['transform'].keys())) == 1
     assert list(pts.attrs['transform'].keys())[0] == 'global'
     assert isinstance(get_transformation(pts, 'global'), Affine)
@@ -86,16 +86,24 @@ def test_pointmodel():
 def test_labelmodel():
     
     # returns DataFrame
-    lbl = generate_labelmodel({'n': 12, 'scale_factors': [2,2,3], 'coordinate_system': 'global'}, 'image')
+    lbl = generate_labelmodel({'n': 12, 'scale_factors': [2,2,3], 'coordinate_system': ['global']}, 'image')
+    assert isinstance(lbl, xarray.DataTree)
+    assert len(lbl) == 4
+
+    # returns DataFrame (3d)
+    lbl = generate_labelmodel({'n': 12, 
+                               'scale_factors': [2,2,3], 
+                               'shape': {'x': 120, 'y': 120, 'z': 120},
+                               'coordinate_system': ['global']}, 'image')
     assert isinstance(lbl, xarray.DataTree)
     assert len(lbl) == 4
 
     # size is not defined
     with pytest.raises(KeyError):
-        lbl = generate_labelmodel({'coordinate_system': 'global'}, 'image')
+        lbl = generate_labelmodel({'coordinate_system': ['global']}, 'image')
 
     # single scale is returned for no scale factor definition
-    lbl = generate_labelmodel({'n': 12, 'coordinate_system': 'global'}, 'image')
+    lbl = generate_labelmodel({'n': 12, 'coordinate_system': ['global']}, 'image')
     assert len(lbl) == 1
 
     # no coordinate system returns element name as coord system and Identity transformation
@@ -105,7 +113,7 @@ def test_labelmodel():
 
     # parses coordinate system
     coord_system = {'global': {'transformations': ['affine'], 'shape': {'x': 2000, 'y': 2000}}}
-    lbl = generate_labelmodel({'n': 12, 'coordinate_system': 'global'}, 'image', coord_system)
+    lbl = generate_labelmodel({'n': 12, 'coordinate_system': ['global']}, 'image', coord_system)
     assert len(list(dict(lbl["scale0"])["image"].attrs['transform'].keys())) == 1
     assert list(dict(lbl["scale0"])["image"].attrs['transform'].keys())[0] == 'global'
     assert isinstance(get_transformation(lbl, 'global'), Affine)

dummy_spatialdata-0.1.8/PKG-INFO

@@ -1,114 +0,0 @@
-Metadata-Version: 2.4
-Name: dummy-spatialdata
-Version: 0.1.8
-Summary: A package for creating arbitrary spatialdata for testing purposes.
-Project-URL: Documentation, https://dummy-spatialdata.readthedocs.io/
-Project-URL: Homepage, https://github.com/BIMSBBioinfo/dummy-spatialdata
-Project-URL: Source, https://github.com/BIMSBBioinfo/dummy-spatialdata
-Author-email: Artür Manukyan <amanukyan.umms@gmail.com>
-License: MIT
-Requires-Python: >=3.12
-Requires-Dist: dummy-anndata>=0.0.3
-Requires-Dist: geopandas
-Requires-Dist: pillow
-Requires-Dist: requests
-Requires-Dist: shapely
-Requires-Dist: spatialdata>=0.5.0
-Provides-Extra: dev
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: twine>=4.0.2; extra == 'dev'
-Provides-Extra: test
-Requires-Dist: coverage; extra == 'test'
-Requires-Dist: pytest; extra == 'test'
-Description-Content-Type: text/markdown
-
-# dummy-spatialdata
-
-Allows generating dummy spatialdata objects, which can be useful for testing purposes.
-
-## Installation
-
-```bash
-pip install dummy-spatialdata
-```
-
-## Example usage
-
-`dummy-spatialdata` is compatible with both spatialdata == 0.5.0 (zarr v2) and 0.7.2 (zarr v3)
-
-Thus please use 
-
-1. `conda create --name dummy_sd_env python==3.12 spatialdata==0.7.2` or 
-2. `conda create --name dummy_sd_env_05 python==3.12 spatialdata==0.5.0 setuptools==75.8.0`
-
-```{python}
-from dummy_spatialdata import generate_dataset
-import dummy_anndata
-import spatialdata_plot as sdp 
-import spatialdata as sd
-import matplotlib.pyplot as plt
-import anndata as ad
-
-# generate anndata
-adata = dummy_anndata.generate_dataset(n_obs=12, n_vars=20)
-
-# generate spatialdata
-sdata = generate_dataset(
-    images = [
-        {'type': 'rgb', 'scale_factors': [2,2,2], 'coordinate_system': 'global'},
-        {'type': 'grayscale', 'coordinate_system': 'global'},
-    ],
-    labels = [
-        {'n': 12, 'scale_factors': [2,2,3], 'coordinate_system': 'global2'},
-        {'n': 12, 'coordinate_system': 'global2'},
-    ], 
-    shapes = [
-        {'n': 12, 'type': 'circle', 'coordinate_system': 'global'},
-        {'n': 20, 'type': 'circle'},
-    ],
-    points = [
-        {'n': 12}
-    ],
-    tables = [
-        {'table': adata, 'element': 'shape', 'element_index': 0}
-    ],
-    coordinate_systems = {
-        'global': {'transformations': ['affine'], 'shape': {'x': 2000, 'y': 2000}},
-        'global2': {'transformations': ['scale', 'translation'], 'shape':{'x': 500, 'y': 500}}
-    },
-    SEED=13
-)
-sdata
-```
-
-```
-SpatialData object
-├── Images
-│     ├── 'image_0': DataTree[cyx] (3, 2000, 2000), (3, 1000, 1000), (3, 500, 500), (3, 250, 250)
-│     └── 'image_1': DataTree[cyx] (1, 2000, 2000)
-├── Labels
-│     ├── 'label_0': DataTree[yx] (500, 500), (250, 250), (125, 125), (41, 41)
-│     └── 'label_1': DataTree[yx] (500, 500)
-├── Points
-│     └── 'point_0': DataFrame with shape: (<Delayed>, 2) (2D points)
-├── Shapes
-│     ├── 'shape_0': GeoDataFrame shape: (12, 2) (2D shapes)
-│     └── 'shape_1': GeoDataFrame shape: (20, 2) (2D shapes)
-└── Tables
-      └── 'table_0': AnnData (12, 20)
-with coordinate systems:
-    ▸ 'global', with elements:
-        image_0 (Images), image_1 (Images), shape_0 (Shapes)
-    ▸ 'global2', with elements:
-        label_0 (Labels), label_1 (Labels)
-    ▸ 'point_0', with elements:
-        point_0 (Points)
-    ▸ 'shape_1', with elements:
-        shape_1 (Shapes)
-```
-
-You can plot the demo data now!
-
-```{python}
-sdata.pl.render_images('image_0').pl.render_shapes('shape_0', color='Gene001', table_name = 'table_0', table_layer = 'float_matrix').pl.show(coordinate_systems = 'global')
-```

dummy_spatialdata-0.1.8/README.md

@@ -1,90 +0,0 @@
-# dummy-spatialdata
-
-Allows generating dummy spatialdata objects, which can be useful for testing purposes.
-
-## Installation
-
-```bash
-pip install dummy-spatialdata
-```
-
-## Example usage
-
-`dummy-spatialdata` is compatible with both spatialdata == 0.5.0 (zarr v2) and 0.7.2 (zarr v3)
-
-Thus please use 
-
-1. `conda create --name dummy_sd_env python==3.12 spatialdata==0.7.2` or 
-2. `conda create --name dummy_sd_env_05 python==3.12 spatialdata==0.5.0 setuptools==75.8.0`
-
-```{python}
-from dummy_spatialdata import generate_dataset
-import dummy_anndata
-import spatialdata_plot as sdp 
-import spatialdata as sd
-import matplotlib.pyplot as plt
-import anndata as ad
-
-# generate anndata
-adata = dummy_anndata.generate_dataset(n_obs=12, n_vars=20)
-
-# generate spatialdata
-sdata = generate_dataset(
-    images = [
-        {'type': 'rgb', 'scale_factors': [2,2,2], 'coordinate_system': 'global'},
-        {'type': 'grayscale', 'coordinate_system': 'global'},
-    ],
-    labels = [
-        {'n': 12, 'scale_factors': [2,2,3], 'coordinate_system': 'global2'},
-        {'n': 12, 'coordinate_system': 'global2'},
-    ], 
-    shapes = [
-        {'n': 12, 'type': 'circle', 'coordinate_system': 'global'},
-        {'n': 20, 'type': 'circle'},
-    ],
-    points = [
-        {'n': 12}
-    ],
-    tables = [
-        {'table': adata, 'element': 'shape', 'element_index': 0}
-    ],
-    coordinate_systems = {
-        'global': {'transformations': ['affine'], 'shape': {'x': 2000, 'y': 2000}},
-        'global2': {'transformations': ['scale', 'translation'], 'shape':{'x': 500, 'y': 500}}
-    },
-    SEED=13
-)
-sdata
-```
-
-```
-SpatialData object
-├── Images
-│     ├── 'image_0': DataTree[cyx] (3, 2000, 2000), (3, 1000, 1000), (3, 500, 500), (3, 250, 250)
-│     └── 'image_1': DataTree[cyx] (1, 2000, 2000)
-├── Labels
-│     ├── 'label_0': DataTree[yx] (500, 500), (250, 250), (125, 125), (41, 41)
-│     └── 'label_1': DataTree[yx] (500, 500)
-├── Points
-│     └── 'point_0': DataFrame with shape: (<Delayed>, 2) (2D points)
-├── Shapes
-│     ├── 'shape_0': GeoDataFrame shape: (12, 2) (2D shapes)
-│     └── 'shape_1': GeoDataFrame shape: (20, 2) (2D shapes)
-└── Tables
-      └── 'table_0': AnnData (12, 20)
-with coordinate systems:
-    ▸ 'global', with elements:
-        image_0 (Images), image_1 (Images), shape_0 (Shapes)
-    ▸ 'global2', with elements:
-        label_0 (Labels), label_1 (Labels)
-    ▸ 'point_0', with elements:
-        point_0 (Points)
-    ▸ 'shape_1', with elements:
-        shape_1 (Shapes)
-```
-
-You can plot the demo data now!
-
-```{python}
-sdata.pl.render_images('image_0').pl.render_shapes('shape_0', color='Gene001', table_name = 'table_0', table_layer = 'float_matrix').pl.show(coordinate_systems = 'global')
-```