poc with working cdf write

geomagio/ImagCDFFactory.py

@@ -15,7 +15,7 @@ from io import BytesIO
 import os
 import sys
 from typing import List, Optional, Union
-
+from datetime import datetime, timezone
 import numpy as np
 from obspy import Stream, Trace, UTCDateTime
 
@@ -121,74 +121,80 @@ class ImagCDFFactory(TimeseriesFactory):
         Note: Parsing from strings is not implemented in this factory.
         """
         raise NotImplementedError('"parse_string" not implemented')
-
     def write_file(self, fh, timeseries: Stream, channels: List[str]):
-        """Write the timeseries data to a file handle in ImagCDF format.
-
-        Parameters:
-        - fh: File handle to write the data.
-        - timeseries: ObsPy Stream containing the geomagnetic data.
-        - channels: List of channels to include in the output file.
-        """
         # Create a temporary file to write the CDF data
         with tempfile.NamedTemporaryFile(delete=False) as tmp_file:
             tmp_file_path = tmp_file.name + ".cdf"
 
         try:
             # Initialize the CDF writer
-            cdf_writer = cdflib.cdfwrite.CDF(tmp_file_path, cdf_spec=None)
+            cdf_writer = cdflib.cdfwrite.CDF(tmp_file_path)
 
-            # Write global attributes (metadata that applies to the entire file)
+            # Write global attributes
             global_attrs = self._create_global_attributes(timeseries, channels)
             cdf_writer.write_globalattrs(global_attrs)
 
-            # Write time variables for each channel
+            # Time variables
             time_vars = self._create_time_stamp_variables(timeseries)
             for ts_name, ts_data in time_vars.items():
+                # Define time variable specification
                 var_spec = {
-                    "Variable": ts_name,
-                    "Data_Type": 33,  # CDF TT2000 data type
-                    "Num_Elements": 1,
-                    "Rec_Vary": True,
-                    "Dim_Sizes": [],
-                    "Var_Type": "zVariable",
+                    'Variable': ts_name,
+                    'Data_Type': 33,  # CDF_TIME_TT2000
+                    'Num_Elements': 1,
+                    'Rec_Vary': True,
+                    'Var_Type': 'zVariable',
+                    'Dim_Sizes': [],
+                    'Sparse': 'no_sparse',
+                    'Compress': 6,
+                    'Pad': None,
                 }
-                print(f"Writing time variable {ts_name} with data length: {len(ts_data)}")
-                cdf_writer.write_var(
-                    var_spec=var_spec,
-                    var_attrs=self._create_time_var_attrs(ts_name),
-                    var_data=ts_data,
-                )
+                # Define time variable attributes
+                var_attrs = self._create_time_var_attrs(ts_name)
+
+                # Write time variable
+                cdf_writer.write_var(var_spec, var_attrs, ts_data)
 
-            # Write geomagnetic data variables
+            # Data variables
             for trace in timeseries:
                 channel = trace.stats.channel
                 var_name = f"GeomagneticField{channel}"
+                data_type = self._get_cdf_data_type(trace)
+                num_elements = 1
+                CDF_CHAR = 51
+                CDF_UCHAR = 52
+                if data_type in [CDF_CHAR, CDF_UCHAR]:  # Handle string types
+                    num_elements = len(trace.data[0]) if len(trace.data) > 0 else 1
+
                 var_spec = {
-                    "Variable": var_name,
-                    "Data_Type": self._get_cdf_data_type(trace),
-                    "Num_Elements": 1,
-                    "Rec_Vary": True,
-                    "Dim_Sizes": [],
-                    "Var_Type": "zVariable",
+                    'Variable': var_name,
+                    'Data_Type': data_type,
+                    'Num_Elements': num_elements,
+                    'Rec_Vary': True,
+                    'Var_Type': 'zVariable',
+                    'Dim_Sizes': [],
+                    'Sparse': 'no_sparse',
+                    'Compress': 6,
+                    'Pad': None,
                 }
-                print(f"Writing data variable {var_name} with data shape: {trace.data.shape}")
-                cdf_writer.write_var(
-                    var_spec=var_spec,
-                    var_attrs=self._create_var_attrs(trace),
-                    var_data=trace.data,
-                )
+
+                var_attrs = self._create_var_attrs(trace)
+
+                # Write data variable
+                cdf_writer.write_var(var_spec, var_attrs, trace.data)
+
+            # Close the CDF writer
+            cdf_writer.close()
 
             # Copy the temporary CDF file to the final file handle
             with open(tmp_file_path, "rb") as tmp:
                 cdf_data = tmp.read()
                 fh.write(cdf_data)
 
-            cdf_writer.close()
-
         finally:
             # Cleanup the temporary file
-            print(tmp_file_path)
+            os.remove(tmp_file_path)
+
 
     def put_timeseries(
         self,
@@ -336,11 +342,11 @@ class ImagCDFFactory(TimeseriesFactory):
             'IagaCode': {0: station},
             'ElementsRecorded': {0: ''.join(channels)},
             'PublicationLevel': {0: publication_level},
-            'PublicationDate': {0: UTCDateTime.now().strftime("%Y-%m-%dT%H:%M:%SZ")},
+            'PublicationDate': {0: [cdflib.cdfepoch.timestamp_to_tt2000(datetime.timestamp(datetime.now(timezone.utc))), "cdf_time_tt2000"]},
             'ObservatoryName': {0: observatory_name},
-            'Latitude': {0: latitude},
-            'Longitude': {0: longitude},
-            'Elevation': {0: elevation},
+            'Latitude': {0: np.array([latitude], dtype=np.float64)},
+            'Longitude': {0: np.array([longitude], dtype=np.float64)},
+            'Elevation': {0: np.array([elevation], dtype=np.float64)},
             'Institution': {0: institution},
             'VectorSensOrient': {0: vector_orientation}, #remove F - because its a calculation, not an element?
             'StandardLevel': {0: 'None'},  # Set to 'None'
@@ -436,7 +442,7 @@ class ImagCDFFactory(TimeseriesFactory):
         return var_spec
 
     def _create_var_attrs(self, trace: Trace) -> dict:
-        print(trace.stats)
+        # print(trace.stats)
         channel = trace.stats.channel
         fieldnam = f"Geomagnetic Field Element {channel}" # “Geomagnetic Field Element ” + the element code or “Temperature ” + the name of the location where the temperature was recorded.
         units = '' # Must be one of “nT”, “Degrees of arc” or “Celsius”