Merge pull request #193 from sandialabs/add-json-converter

Add json converter

Author: rsbrost

pyscan/drivers/testing/driver_test_logs/test_instrument_driver_test_log.txt

@@ -1 +1 @@
-Passed with test_instrument_driver version v0.1.0 tested on pyscan version v0.5.3 at 2024-07-05 11:41:28
+Passed with test_instrument_driver version v0.1.0 tested on pyscan version v0.5.4 at 2024-07-09 09:46:08

pyscan/drivers/testing/driver_test_logs/test_voltage_test_log.txt

@@ -1 +1 @@
-Passed with test_voltage version v0.1.0 tested on pyscan version v0.5.3 at 2024-07-05 11:41:28
+Passed with test_voltage version v0.1.0 tested on pyscan version v0.5.4 at 2024-07-09 09:46:08

pyscan/general/__init__.py

@@ -1,16 +1,15 @@
+# objects
+from .item_attribute import ItemAttribute
+from .pyscan_json_encoder import PyscanJSONEncoder
 
 # methods
 from .d_range import drange
 from .first_string import first_string
 from .is_list_type import is_list_type
 from .is_numeric_type import is_numeric_type
 from .quadrature_sum import quadrature_sum
-from .recursive_to_dict import recursive_to_dict
-from .recursive_to_item_attribute import recursive_to_itemattribute
 from .same_length import same_length
 from .set_difference import set_difference
 from .stack_or_append import stack_or_append
 from .get_pyscan_version import get_pyscan_version
-
-# objects
-from .item_attribute import ItemAttribute
+from .pyscan_json_decoder import PyscanJSONDecoder

pyscan/general/pyscan_json_decoder.py

@@ -0,0 +1,28 @@
+from pyscan.general import ItemAttribute
+import json
+
+
+class PyscanJSONDecoder(json.JSONDecoder):
+    def __init__(self, *args, **kwargs):
+        super().__init__(object_hook=self.item_attribute_object_hook, *args, **kwargs)
+
+    def item_attribute_object_hook(self, data):
+        '''
+        Function to be used as the object_hook in json.loads to convert dictionaries
+        into ItemAttribute objects.
+
+        Parameters
+        ----------
+        data : dict
+            The dictionary to convert.
+
+        Returns
+        -------
+        ItemAttribute
+        '''
+        if type(data) is dict:
+            new_data = ItemAttribute(data)
+        else:
+            new_data = data
+
+        return new_data

pyscan/general/pyscan_json_encoder.py

@@ -0,0 +1,72 @@
+import json
+import numpy as np
+from pyscan.general.item_attribute import ItemAttribute
+from pyscan.drivers.instrument_driver import InstrumentDriver
+import inspect
+from pathlib import Path, WindowsPath
+
+
+class PyscanJSONEncoder(json.JSONEncoder):
+    """
+    A custom JSON encoder subclass that extends json.JSONEncoder to handle additional Python data types
+    not supported by the default JSON encoder. This includes handling of custom objects, numpy data types,
+    function objects, and pathlib Path objects, among others.
+
+    The encoder attempts to serialize various non-standard objects to a JSON-compatible format, applying
+    specific conversions based on the object type. If an object is already JSON serializable, the encoder
+    falls back to the default method provided by the superclass.
+    """
+
+    def default(self, obj, debug=False):
+        """
+        Convert non-serializable objects to a serializable format.
+
+        Parameters:
+        - obj: The object to serialize.
+
+        Returns:
+        - A serializable representation of `obj` or raises a TypeError if the object cannot be serialized.
+        """
+        if debug is True:
+            print(f"Processing object {obj} of type: {type(obj)}")
+            try:
+                print(f"Obj name is: {obj.__name__}")
+            except:
+                pass
+        # keys_to_skip = {'logger', 'expt_thread', 'data_path', 'instrument', 'module_id_string', 'spec'}
+
+        if type(obj) is type:
+            return obj.__name__
+        elif isinstance(obj, (InstrumentDriver, ItemAttribute)):
+            if debug is True:
+                print(f"obj {obj} was instance of InstrumentDriver and or ItemAttribute.")
+            return obj.__dict__
+        elif isinstance(obj, (range, tuple)):
+            if debug is True:
+                print(f"obj {obj} was instance of {type(obj)}.")
+            return list(obj)
+        # Handle numpy integers
+        elif isinstance(obj, np.integer):
+            if debug is True:
+                print(f"Object {obj} is a numpy integer, converting to int.")
+            return int(obj)
+        # Handle numpy floating values
+        elif isinstance(obj, np.floating):
+            if debug is True:
+                print(f"Object {obj} is a numpy floating value, converting to float.")
+            return float(obj)
+        # Handle numpy arrays
+        elif isinstance(obj, np.ndarray):
+            if debug is True:
+                print(f"Object {obj} is a numpy array, converting to list.")
+            return obj.tolist()
+        elif callable(obj):
+            if debug is True:
+                print(f"obj {obj} is a function, returning source code.")
+            return inspect.getsource(obj)  # Talk with Andy about this and perhaps implementing in load_expt?
+        elif isinstance(obj, (WindowsPath, Path)):  # This covers both WindowsPath and PosixPath
+            if debug is True:
+                print(f"obj {obj} is a Path or WindowsPath, returning string of the path.")
+            return str(obj)
+        else:
+            return super().default(obj)

pyscan/general/recursive_to_dict.py

@@ -6,9 +6,9 @@
 from threading import Thread as thread
 from time import strftime
 from pyscan.general import (ItemAttribute,
-                            recursive_to_dict,
                             is_list_type)
 from pyscan.measurement.scans import PropertyScan, RepeatScan
+from pyscan.general.pyscan_json_encoder import PyscanJSONEncoder
 
 
 class AbstractExperiment(ItemAttribute):
@@ -235,11 +235,9 @@ def save_metadata(self):
         save_path = self.runinfo.data_path / '{}.hdf5'.format(self.runinfo.long_name)
         save_name = str(save_path.absolute())
 
-        data = recursive_to_dict(self.__dict__)
-
         with h5py.File(save_name, 'a') as f:
-            f.attrs['runinfo'] = json.dumps(data['runinfo'])
-            f.attrs['devices'] = json.dumps(data['devices'])
+            f.attrs['runinfo'] = json.dumps(self.runinfo, cls=PyscanJSONEncoder)
+            f.attrs['devices'] = json.dumps(self.devices, cls=PyscanJSONEncoder)
 
     def start_thread(self):
         '''Starts experiment as a background thread, this works in conjunction with live plot

pyscan/general/recursive_to_item_attribute.py

@@ -3,7 +3,8 @@
 import pickle
 import json
 from pathlib import Path
-from pyscan.general import ItemAttribute, recursive_to_itemattribute
+from pyscan.general.item_attribute import ItemAttribute
+from pyscan.general.pyscan_json_decoder import PyscanJSONDecoder
 
 
 def load_experiment(file_name):
@@ -57,11 +58,9 @@ def load_experiment(file_name):
         expt.devices = ItemAttribute()
 
         f = h5py.File('{}'.format(file_name), 'r')
-        runinfo = json.loads(f.attrs['runinfo'])
-        expt.runinfo = recursive_to_itemattribute(runinfo)
+        expt.runinfo = json.loads(f.attrs['runinfo'], cls=PyscanJSONDecoder)
 
-        devices = json.loads(f.attrs['devices'])
-        expt.devices = recursive_to_itemattribute(devices)
+        expt.devices = json.loads(f.attrs['devices'], cls=PyscanJSONDecoder)
 
         for key, value in f.items():
             expt[key] = (f[key][:]).astype('float64')