Merge pull request #170 from RichieHakim/dev

Dev
RichieHakim · Jan 28, 2024 · 5196f4a · 5196f4a
2 parents a3caf92 + 41f534c
commit 5196f4a
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -36,7 +36,7 @@ jobs:
           windows-2022,
           windows-2019,
           # # macos-latest,
-          # macos-12.0,
+          macos-12,
           macos-11.0,
           # macos-10.15,
         ]

diff --git a/requirements.txt b/requirements.txt
@@ -5,18 +5,18 @@ kymatio==0.3.0
 matplotlib==3.8.2
 natsort==8.4.0
 numpy==1.26.3
-opencv_contrib_python==4.8.1.78
-optuna==3.4.0
+opencv_contrib_python<=4.9.0.80
+optuna==3.5.0
 Pillow==10.2.0
 pytest==7.4.4
 scikit_learn==1.4.0
 scipy==1.12.0
-seaborn==0.13.1
+seaborn==0.13.2
 sparse==0.15.1
 tqdm==4.66.1
 umap_learn==0.5.5
 xxhash==3.4.1
-bokeh==3.3.3
+bokeh==3.3.4
 psutil==5.9.8
 py_cpuinfo==9.0.0
 GPUtil==1.4.0
@@ -25,7 +25,7 @@ mat73==0.62
 torch==2.1.2
 torchvision==0.16.2
 torchaudio==2.1.2
-selenium==4.16.0
+selenium==4.17.2
 skl2onnx==1.16.0
 onnx==1.15.0
 onnxruntime==1.16.3

diff --git a/roicat/__init__.py b/roicat/__init__.py
@@ -13,4 +13,4 @@
 for pkg in __all__:
     exec('from . import ' + pkg)
 
-__version__ = '1.1.28'
+__version__ = '1.1.29'
diff --git a/roicat/helpers.py b/roicat/helpers.py
@@ -200,6 +200,88 @@ def flatten_dict(d: MutableMapping, parent_key: str = '', sep: str ='.') -> Muta
             items.append((new_key, v))
     return dict(items)
 
+## parameter dictionary helpers ##
+
+def fill_in_dict(
+    d: Dict, 
+    defaults: Dict,
+    verbose: bool = True,
+    hierarchy: List[str] = ['dict'], 
+):
+    """
+    In-place. Fills in dictionary ``d`` with values from ``defaults`` if they
+    are missing. Works hierachically.
+    RH 2023
+
+    Args:
+        d (Dict):
+            Dictionary to fill in.
+            In-place.
+        defaults (Dict):
+            Dictionary of defaults.
+        verbose (bool):
+            Whether to print messages.
+        hierarchy (List[str]):
+            Used internally for recursion.
+            Hierarchy of keys to d.
+    """
+    from copy import deepcopy
+    for key in defaults:
+        if key not in d:
+            print(f"Key '{key}' not found in params dictionary: {' > '.join([f'{str(h)}' for h in hierarchy])}. Using default value: {defaults[key]}") if verbose else None
+            d.update({key: deepcopy(defaults[key])})
+        elif isinstance(defaults[key], dict):
+            assert isinstance(d[key], dict), f"Key '{key}' is a dict in defaults, but not in params. {' > '.join([f'{str(h)}' for h in hierarchy])}."
+            fill_in_dict(d[key], defaults[key], hierarchy=hierarchy+[key])
+
+
+def check_keys_subset(d, default_dict, hierarchy=['defaults']):
+    """
+    Checks that the keys in d are all in default_dict. Raises an error if not.
+    RH 2023
+
+    Args:
+        d (Dict):
+            Dictionary to check.
+        default_dict (Dict):
+            Dictionary containing the keys to check against.
+        hierarchy (List[str]):
+            Used internally for recursion.
+            Hierarchy of keys to d.
+    """
+    default_keys = list(default_dict.keys())
+    for key in d.keys():
+        assert key in default_keys, f"Parameter '{key}' not found in defaults dictionary: {' > '.join([f'{str(h)}' for h in hierarchy])}."
+        if isinstance(default_dict[key], dict) and isinstance(d[key], dict):
+            check_keys_subset(d[key], default_dict[key], hierarchy=hierarchy+[key])
+
+
+def prepare_params(params, defaults, verbose=True):
+    """
+    Does the following:
+        * Checks that all keys in ``params`` are in ``defaults``.
+        * Fills in any missing keys in ``params`` with values from ``defaults``.
+        * Returns a deepcopy of the filled-in ``params``.
+
+    Args:
+        params (Dict):
+            Dictionary of parameters.
+        defaults (Dict):
+            Dictionary of defaults.
+        verbose (bool):
+            Whether to print messages.
+    """
+    from copy import deepcopy
+    ## Check inputs
+    assert isinstance(params, dict), f"p must be a dict. Got {type(params)} instead."
+    ## Make sure all the keys in p are valid
+    check_keys_subset(params, defaults)
+    ## Fill in any missing keys with defaults
+    params_out = deepcopy(params)
+    fill_in_dict(params_out, defaults, verbose=verbose)
+
+    return params_out
+
 
 ######################################################################################################################################
 ####################################################### MATH FUNCTIONS ###############################################################

diff --git a/roicat/pipelines.py b/roicat/pipelines.py
@@ -30,12 +30,12 @@ def pipeline_tracking(params: dict):
                 pipeline.
             params (dict):
                 Parameters used in the pipeline. See
-                ``roicat.util.prepare_params()`` for details.
+                ``roicat.helpers.prepare_params()`` for details.
     """
 
     ## Prepare params
     defaults = util.get_default_parameters(pipeline='tracking')
-    params = util.prepare_params(params, defaults, verbose=True)
+    params = helpers.prepare_params(params, defaults, verbose=True)
     display(params)
 
     ## Prepare state variables

diff --git a/roicat/util.py b/roicat/util.py
@@ -250,84 +250,6 @@ def get_default_parameters(
 
     return out
 
-def fill_in_params(
-    d: Dict, 
-    defaults: Dict,
-    verbose: bool = True,
-    hierarchy: List[str] = ['params'], 
-):
-    """
-    In-place. Fills in dictionary ``d`` with values from ``defaults`` if they
-    are missing. Works hierachically.
-    RH 2023
-
-    Args:
-        d (Dict):
-            Dictionary to fill in.
-            In-place.
-        defaults (Dict):
-            Dictionary of defaults.
-        verbose (bool):
-            Whether to print messages.
-        hierarchy (List[str]):
-            Used internally for recursion.
-            Hierarchy of keys to d.
-    """
-    from copy import deepcopy
-    for key in defaults:
-        if key not in d:
-            print(f"Parameter '{key}' not found in params dictionary: {' > '.join([f'{str(h)}' for h in hierarchy])}. Using default value: {defaults[key]}") if verbose else None
-            d.update({key: deepcopy(defaults[key])})
-        elif isinstance(defaults[key], dict):
-            assert isinstance(d[key], dict), f"Parameter '{key}' must be a dictionary."
-            fill_in_params(d[key], defaults[key], hierarchy=hierarchy+[key])
-
-def check_keys_subset(d, default_dict, hierarchy=['defaults']):
-    """
-    Checks that the keys in d are all in default_dict. Raises an error if not.
-    RH 2023
-
-    Args:
-        d (Dict):
-            Dictionary to check.
-        default_dict (Dict):
-            Dictionary containing the keys to check against.
-        hierarchy (List[str]):
-            Used internally for recursion.
-            Hierarchy of keys to d.
-    """
-    default_keys = list(default_dict.keys())
-    for key in d.keys():
-        assert key in default_keys, f"Parameter '{key}' not found in defaults dictionary: {' > '.join([f'{str(h)}' for h in hierarchy])}."
-        if isinstance(default_dict[key], dict) and isinstance(d[key], dict):
-            check_keys_subset(d[key], default_dict[key], hierarchy=hierarchy+[key])
-
-def prepare_params(params, defaults, verbose=True):
-    """
-    Does the following:
-        * Checks that all keys in ``params`` are in ``defaults``.
-        * Fills in any missing keys in ``params`` with values from ``defaults``.
-        * Returns a deepcopy of the filled-in ``params``.
-
-    Args:
-        params (Dict):
-            Dictionary of parameters.
-        defaults (Dict):
-            Dictionary of defaults.
-        verbose (bool):
-            Whether to print messages.
-    """
-    from copy import deepcopy
-    ## Check inputs
-    assert isinstance(params, dict), f"p must be a dict. Got {type(params)} instead."
-    ## Make sure all the keys in p are valid
-    check_keys_subset(params, defaults)
-    ## Fill in any missing keys with defaults
-    params_out = deepcopy(params)
-    fill_in_params(params_out, defaults, verbose=verbose)
-
-    return params_out
-
 
 def system_info(verbose: bool = False,) -> Dict:
     """

diff --git a/setup.py b/setup.py
@@ -1,11 +1,14 @@
 ## setup.py file for roicat
 from pathlib import Path
+import copy
+import platform
 
 from distutils.core import setup
-import copy
 
+## Get the parent directory of this file
 dir_parent = Path(__file__).parent
 
+## Get requirements from requirements.txt
 def read_requirements():
     with open(str(dir_parent / "requirements.txt"), "r") as req:
         content = req.read()  ## read the file
@@ -19,15 +22,33 @@ def read_requirements():
     requirements = [req.replace(",", "").replace("\"", "").replace("\'", "").strip() for req in requirements]
 
     return requirements
-
 deps_all = read_requirements()
 
+
 ## Dependencies: latest versions of requirements
 ### remove everything starting and after the first =,>,<,! sign
 deps_names = [req.split('=')[0].split('>')[0].split('<')[0].split('!')[0] for req in deps_all]
 deps_all_dict = dict(zip(deps_names, deps_all))
 
-deps_all_latest = copy.deepcopy(deps_names)
+deps_all_latest = dict(zip(deps_names, deps_names))
+
+
+# Operating system specific dependencies
+# OpenCV >= 4.9 is not supported on macOS < 12
+system, version_macos = platform.system(), platform.mac_ver()[0]
+print(f"System: {system}, macOS version: {version_macos}")
+if (system == "Darwin"):
+    # Safely convert version string components to integers
+    version_parts = version_macos.split('.')
+    version_major_macos = int(version_parts[0])
+
+    # Check macOS version and adjust the OpenCV version accordingly
+    if (version_major_macos < 12) and ('opencv_contrib_python' in deps_all_dict):
+        version_opencv_macos_sub12 = "opencv_contrib_python<=4.8.1.78"
+        print(f"Detected macOS version {version_major_macos}, which is < 12. Installing an older version of OpenCV: {version_opencv_macos_sub12}")
+        deps_all_dict['opencv_contrib_python'] = version_opencv_macos_sub12
+        deps_all_latest['opencv_contrib_python'] = version_opencv_macos_sub12
+
 
 ## Make different versions of dependencies
 ### Also pull out the version number from the requirements (specified in deps_all_dict values).
@@ -53,30 +74,30 @@ def read_requirements():
     'psutil',
     'py_cpuinfo',
     'GPUtil',
+    'skl2onnx',
+    'onnx',
+    'onnxruntime',
+    'opencv_contrib_python',
 ]]
 
 deps_classification = [deps_all_dict[dep] for dep in [
-    'opencv_contrib_python',
     'umap_learn',
     'bokeh',
     'holoviews[recommended]',
     'jupyter_bokeh',
-    'skl2onnx',
-    'onnx',
-    'onnxruntime',
 ]] + deps_core
 
 deps_tracking = [deps_all_dict[dep] for dep in [
-    'opencv_contrib_python',
     'hdbscan',
     'kymatio',
 ]] + deps_core
 
+
 ## Get README.md
 with open(str(dir_parent / "README.md"), "r") as f:
     readme = f.read()
 
-## Get version number
+## Get ROICaT version number
 with open(str(dir_parent / "roicat" / "__init__.py"), "r") as f:
     for line in f:
         if line.startswith("__version__"):
@@ -103,8 +124,8 @@ def read_requirements():
 
     install_requires=[],
     extras_require={
-        'all': deps_all,
-        'all_latest': deps_all_latest,
+        'all': list(deps_all_dict.values()),
+        'all_latest': list(deps_all_latest.values()),
         'core': deps_core,
         'classification': deps_classification,
         'tracking': deps_tracking,

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -62,7 +62,7 @@ def test_pipeline_tracking_simple(dir_data_test):
             },
         },
     }
-    params = util.prepare_params(params_partial, defaults)
+    params = helpers.prepare_params(params_partial, defaults)
     results, run_data, params = pipelines.pipeline_tracking(params)
 
     #check that results fields are not empty