diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 0985597c37f0e3ff6912b03eaceb009a6ad0ab96..4e212579a625d08143fbf64bce5979c40976080c 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -7,7 +7,7 @@ from typing import List, Optional, Tuple, Union
from obspy.core import Stream, UTCDateTime
-from geomagio.ImagCDFFactory import ImagCDFFactory
+from geomagio.imagcdf.ImagCDFFactory import ImagCDFFactory
from .algorithm import Algorithm, algorithms, AlgorithmException, FilterAlgorithm
from .DerivedTimeseriesFactory import DerivedTimeseriesFactory
@@ -28,7 +28,7 @@ from . import vbf
from . import xml
from . import covjson
from . import netcdf
-from geomagio.ImagCDFFactory import ImagCDFFactory
+from geomagio.imagcdf.ImagCDFFactory import ImagCDFFactory
class Controller(object):
@@ -635,7 +635,7 @@ def get_output_factory(args):
elif output_type == "plot":
output_factory = PlotTimeseriesFactory()
elif output_type == "imagcdf":
- output_factory = ImagCDFFactory()
+ output_factory = ImagCDFFactory(**output_factory_args)
else:
# stream compatible factories
if output_type == "binlog":
diff --git a/geomagio/ImagCDFFactory.py b/geomagio/imagcdf/ImagCDFFactory.py
similarity index 93%
rename from geomagio/ImagCDFFactory.py
rename to geomagio/imagcdf/ImagCDFFactory.py
index af603201de1773abdfcbe65836f290142e28d590..a7838f14fb8283ae15d138bee61807af200efeba 100644
--- a/geomagio/ImagCDFFactory.py
+++ b/geomagio/imagcdf/ImagCDFFactory.py
@@ -25,10 +25,10 @@ from sqlalchemy import true
from geomagio.TimeseriesFactory import TimeseriesFactory
from geomagio.api.ws.Element import TEMPERATURE_ELEMENTS_ID
-from .geomag_types import DataInterval, DataType
-from .TimeseriesFactoryException import TimeseriesFactoryException
-from . import TimeseriesUtility
-from . import Util
+from ..geomag_types import DataInterval, DataType
+from ..TimeseriesFactoryException import TimeseriesFactoryException
+from .. import TimeseriesUtility
+from .. import Util
import cdflib
from cdflib.cdfwrite import CDF as CDFWriter
@@ -93,6 +93,7 @@ class ImagCDFFactory(TimeseriesFactory):
"""
isUniqueTimes = True # used to determine depend_0 and CDF Time Variable Name
+ NONSTANDARD_ELEMENTS = TEMPERATURE_ELEMENTS_ID
def __init__(
self,
@@ -123,13 +124,6 @@ class ImagCDFFactory(TimeseriesFactory):
urlInterval=urlInterval,
)
- def parse_string(self, data: str, **kwargs):
- """Parse ImagCDF formatted string data into a Stream.
-
- 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]):
# Create a temporary file to write the CDF data
with tempfile.NamedTemporaryFile(delete=False, suffix=".cdf") as tmp_file:
@@ -164,7 +158,7 @@ class ImagCDFFactory(TimeseriesFactory):
"Rec_Vary": True,
"Var_Type": "zVariable",
"Dim_Sizes": [],
- "Sparse": "no_sparse", # no_sparse because there should not be time gaps.
+ "Sparse": "no_sparse", # no_sparse because there should not be time gaps. (Time stamps must represent a regular time series with no missing values in the series)
"Compress": 9,
"Pad": None,
}
@@ -178,11 +172,10 @@ class ImagCDFFactory(TimeseriesFactory):
temperature_index = 0
for trace in timeseries:
channel = trace.stats.channel
- if channel in TEMPERATURE_ELEMENTS_ID:
- temperature_index += 1 # MUST INCREMENT INDEX BEFORE USING
- var_name = f"Temperature{temperature_index}"
- else:
- var_name = f"GeomagneticField{channel}"
+ var_name = f"GeomagneticField{channel}"
+ # if channel in REAL_TEMPERATURE:
+ # temperature_index += 1 # MUST INCREMENT INDEX BEFORE USING
+ # var_name = f"Temperature{temperature_index}"
data_type = self._get_cdf_data_type(trace)
num_elements = 1
if data_type in [
@@ -258,8 +251,8 @@ class ImagCDFFactory(TimeseriesFactory):
observatory = stats.station
starttime = starttime or stats.starttime
endtime = endtime or stats.endtime
-
# Split data into intervals if necessary
+
urlIntervals = Util.get_intervals(
starttime=starttime, endtime=endtime, size=self.urlInterval
)
@@ -295,7 +288,6 @@ class ImagCDFFactory(TimeseriesFactory):
starttime=interval_start,
endtime=interval_end,
)
-
# Check if the file already exists to merge data
if os.path.isfile(url_file):
try:
@@ -325,13 +317,13 @@ class ImagCDFFactory(TimeseriesFactory):
)
# Proceed with new data
- # Pad the data with NaNs to ensure it fits the interval
+ # Pad the data to ensure it fits the interval
url_data.trim(
starttime=interval_start,
endtime=interval_end,
nearest_sample=False,
pad=True,
- fill_value=np.nan,
+ fill_value=99_999, # FILLVAL
)
# Write the data to the CDF file
@@ -539,6 +531,7 @@ class ImagCDFFactory(TimeseriesFactory):
def _create_time_stamp_variables(self, timeseries: Stream) -> dict:
vector_times = None
scalar_times = None
+ nonstandard_times = None
temperature_times = {}
temperature_index = 1
@@ -571,14 +564,21 @@ class ImagCDFFactory(TimeseriesFactory):
raise ValueError(
"Time stamps for scalar channels are not the same."
)
- elif channel in TEMPERATURE_ELEMENTS_ID:
- ts_key = f"Temperature{temperature_index}Times"
- if ts_key not in temperature_times:
- temperature_times[ts_key] = tt2000_times
- temperature_index += 1
+ # elif channel in REAL_TEMPERATURES:
+ # ts_key = f"Temperature{temperature_index}Times"
+ # if ts_key not in temperature_times:
+ # temperature_times[ts_key] = tt2000_times
+ # temperature_index += 1
+ # else:
+ # temperature_times[ts_key] = tt2000_times
+ elif channel in self.NONSTANDARD_ELEMENTS:
+ if scalar_times is None:
+ nonstandard_times = tt2000_times
else:
- temperature_times[ts_key] = tt2000_times
-
+ if not np.array_equal(scalar_times, tt2000_times):
+ raise ValueError(
+ "Time stamps for nonstandard channels are not the same."
+ )
time_vars = {}
if vector_times is not None:
time_vars["GeomagneticVectorTimes"] = vector_times
@@ -587,16 +587,28 @@ class ImagCDFFactory(TimeseriesFactory):
if temperature_times:
time_vars.update(temperature_times)
+ isNonStandard = nonstandard_times is not None
+ if isNonStandard:
+ time_vars["NonstandardTimes"] = nonstandard_times
+
last_times = []
+
self.isUniqueTimes = (
len(time_vars) == 1
- ) # true if only one set of times, else default to false.
+ ) # (true if is a single time stamp variable in the file)
for index, times in enumerate(time_vars.values()):
if index > 0:
self.isUniqueTimes = not np.array_equal(last_times, times)
last_times = times
-
- return time_vars if self.isUniqueTimes else {"DataTimes": last_times}
+ if self.isUniqueTimes and isNonStandard and len(time_vars) > 2:
+ raise ValueError(
+ f"Time stamps must be the same for all channels when using nonstandard channels: {','.join(self.NONSTANDARD_ELEMENTS)}"
+ )
+ return (
+ {"DataTimes": last_times}
+ if isNonStandard or not self.isUniqueTimes
+ else time_vars
+ )
def _create_var_spec(
self,
@@ -660,9 +672,13 @@ class ImagCDFFactory(TimeseriesFactory):
validmax = 90.0 # The magnetic field vector can point straight down (+90°), horizontal (0°), or straight up (-90°).
elif channel in TEMPERATURE_ELEMENTS_ID:
units = "Celsius"
- fieldnam = f"Temperature {temperature_index} {trace.stats.location}"
validmin = -273.15 # absolute zero
validmax = 79_999
+ # elif channel in [REAL_TEMPERATURES]:
+ # units = "Celsius"
+ # fieldnam = f"Temperature {temperature_index} {trace.stats.location}"
+ # validmin = -273.15 # absolute zero
+ # validmax = 79_999
elif channel in ["F", "S"]:
units = "nT"
validmin = (
@@ -675,12 +691,14 @@ class ImagCDFFactory(TimeseriesFactory):
validmax = 79_999.0
# Determine DEPEND_0 based on channel type
- if channel in self._get_vector_elements():
+ if not isUniqueTimes:
+ depend_0 = "DataTimes"
+ elif channel in self._get_vector_elements():
depend_0 = "GeomagneticVectorTimes"
elif channel in self._get_scalar_elements():
depend_0 = "GeomagneticScalarTimes"
- elif channel in TEMPERATURE_ELEMENTS_ID:
- depend_0 = f"Temperature{temperature_index}Times"
+ # elif channel in REAL_TEMPERATURES:
+ # depend_0 = f"Temperature{temperature_index}Times"
var_attrs = {
"FIELDNAM": fieldnam,
@@ -688,10 +706,10 @@ class ImagCDFFactory(TimeseriesFactory):
"FILLVAL": 99999.0,
"VALIDMIN": validmin,
"VALIDMAX": validmax,
- "DEPEND_0": depend_0 if isUniqueTimes else "DataTimes",
+ "DEPEND_0": depend_0,
"DISPLAY_TYPE": "time_series",
"LABLAXIS": channel,
- "DATA_INTERVAL_TYPE": trace.stats.data_interval_type,
+ "DATA_INTERVAL_TYPE": trace.stats.data_interval_type, # optional
}
return var_attrs
@@ -953,10 +971,11 @@ class ImagCDFFactory(TimeseriesFactory):
# If the urlTemplate doesn't support placeholders, assume 'file://' scheme
if self.urlTemplate.startswith("file://"):
- base_path = self.urlTemplate[7:] # Strip "file://"
+ base_path = self.urlTemplate[7:]
if not base_path or base_path == "{obs}_{dt}_{t}.cdf":
base_path = os.getcwd() # Default to current working directory
- return os.path.join(base_path, filename)
+ return os.path.join(base_path, filename)
+ return os.path.join(self.urlTemplate, filename)
# Unsupported URL scheme
raise TimeseriesFactoryException(