das2numpy 1.1__tar.gz → 1.1.2__tar.gz

{das2numpy-1.1/src/das2numpy.egg-info → das2numpy-1.1.2}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: das2numpy
-Version: 1.1
+Version: 1.1.2
 Summary: A simple and universal package for loading large amounts of distributed acoustic sensing (DAS) data.
 Author-email: Erik Genthe <erik.genthe@desy.de>
-Project-URL: Homepage, https://git.physnet.uni-hamburg.de/wave/das2numpy
+Project-URL: Homepage, https://gitlab.desy.de/wave/tools/das2numpy
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent

{das2numpy-1.1 → das2numpy-1.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "das2numpy"
-version = "1.1"
+version = "1.1.2"
 authors = [
   { name="Erik Genthe", email="erik.genthe@desy.de" },
 ]
@@ -20,4 +20,4 @@ dependencies = [
     "numpy", "ffmpeg-python", "h5py", "scipy", "numba",
 ]
 [project.urls]
-Homepage = "https://git.physnet.uni-hamburg.de/wave/das2numpy"
+Homepage = "https://gitlab.desy.de/wave/tools/das2numpy"

{das2numpy-1.1 → das2numpy-1.1.2}/src/das2numpy/setups/flac_200hz.py

@@ -90,7 +90,8 @@ def load_file(file_path, file_timestamp, t_start, t_end, t_step, channel_start,
                 + "execute 'module load maxwell ffmpeg'")
     
     # Trim data
-    data = data[:, channel_start:channel_end]
+    if channel_end != -1: # Avoids that last channel is missing when channel_end == -1
+        data = data[:, channel_start:channel_end]
 
     data = data.astype(NP.float32) #This needs to hapen before the binning step!
 

{das2numpy-1.1 → das2numpy-1.1.2}/src/das2numpy/setups/light_tdms_reader.py

@@ -178,7 +178,6 @@ class TdmsReader(object):
         # Check if already hold properties in memory
         if self._properties is None:
             self._properties = self._read_properties()
-        print(self._properties)
         dict = {}
         for key, _, value in self._properties:
             dict[key] = value

{das2numpy-1.1 → das2numpy-1.1.2}/src/das2numpy/setups/optasense_b35idefix.py

@@ -29,6 +29,8 @@ def _load_from_h5(file_path, rel_t_start, rel_t_end, t_step, channel_start, chan
     data = file['Acquisition']['Raw[0]']['RawData'] # Data is not loaded into memory at this point! (Lazy evaluation)
 
     # At this point the data gets loaded into memory.
+    if channel_end != -1: # Avoids that last channel is missing when channel_end == -1
+        channel_end = None
     data = data[
             channel_start : channel_end : channel_step, 
             rel_t_start : rel_t_end : t_step

{das2numpy-1.1 → das2numpy-1.1.2}/src/das2numpy/setups/silixa.py

@@ -63,6 +63,8 @@ def load_file(file_path, file_timestamp, t_start, t_end, t_step, channel_start,
                     f"    Filepath: {file_path}.")
             return NP.zeros(shape=[0, 0])
         assert rel_t_end == -1 or rel_t_end > rel_t_start, f"rel_t_start={rel_t_start}, rel_t_end={rel_t_end}."
+        if channel_end == -1: # Avoids that last channel is missing when channel_end == -1
+            channel_end = None
         data = data[rel_t_start:rel_t_end, channel_start:channel_end]
 
 

{das2numpy-1.1 → das2numpy-1.1.2/src/das2numpy.egg-info}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: das2numpy
-Version: 1.1
+Version: 1.1.2
 Summary: A simple and universal package for loading large amounts of distributed acoustic sensing (DAS) data.
 Author-email: Erik Genthe <erik.genthe@desy.de>
-Project-URL: Homepage, https://git.physnet.uni-hamburg.de/wave/das2numpy
+Project-URL: Homepage, https://gitlab.desy.de/wave/tools/das2numpy
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent

{das2numpy-1.1 → das2numpy-1.1.2}/src/das2numpy.egg-info/SOURCES.txt

@@ -15,6 +15,4 @@ src/das2numpy.egg-info/top_level.txt
 src/das2numpy/setups/flac_200hz.py
 src/das2numpy/setups/light_tdms_reader.py
 src/das2numpy/setups/optasense_b35idefix.py
-src/das2numpy/setups/optasense_b35idefix_fast.py
-src/das2numpy/setups/silixa.py
-src/das2numpy/setups/silixa_200hz.py
+src/das2numpy/setups/silixa.py

das2numpy-1.1/src/das2numpy/setups/optasense_b35idefix_fast.py

@@ -1,111 +0,0 @@
-""" Deprecated
-"""
-
-from math import ceil, floor
-import mmap
-from os import path as P
-import numpy as NP
-import h5py as H5PY
-import datetime as DT
-from time import time
-from filefinder import FileFinder, to_posix_timestamp_ms
-from chunk import Chunk
-
-#/wave/seismic-work/markhoff/pilot/data/cache/7wave7seismic-rawdata7OPTA7Disk27DESY-Rec-9-GL8m-Chan10000_2021-05-28T06_01_36+01007DESY-Rec-9-GL8m-Chan10000_2021-05-28T194319Z.h5.bin
-FILE_TIME_SAMPLE_AMOUNT = 60000
-CHANNEL_AMOUNT = 10000
-DATA_ROOT = "/wave/seismic-work/markhoff/pilot/data/cache"
-assert P.isdir(DATA_ROOT)
-
-def _filename_to_posix_timestamp(file_name:str) -> int:
-    return to_posix_timestamp_ms(DT.datetime.strptime(file_name[-25:], "%Y-%m-%dT%H%M%SZ.h5.bin"))
-
-
-
-def _load_from_h5(file_path, rel_t_start, rel_t_end, t_step, channel_start, channel_end, channel_step) -> NP.ndarray:
-    """ Internal helper function """
-    #file_handle = open(file_path, 'rb')
-    #file:H5PY.File = H5PY.File(file_handle, 'r')
-    #data = file['Acquisition']['Raw[0]']['RawData'] # Data is not loaded into memory at this point! (Lazy evaluation)
-#
-    ## At this point the data gets loaded into memory.
-    #data = data[
-    #        channel_start : channel_end : channel_step, 
-    #        rel_t_start : rel_t_end : t_step
-    #]
-
-    DTYPE_SIZE = 4
-    data = None
-    #if channel_step == 1:
-    #    data = NP.fromfile(
-    #        file_path,
-    #        dtype = NP.int32,
-    #        offset = channel_start * FILE_TIME_SAMPLE_AMOUNT * DTYPE_SIZE,
-    #        count = (channel_end-channel_start) * FILE_TIME_SAMPLE_AMOUNT
-    #    )
-    #    data.shape = (channel_end-channel_start, FILE_TIME_SAMPLE_AMOUNT)
-    #    data = data[:, rel_t_start:rel_t_end:t_step]
-    #else:
-    #    data = NP.ndarray(
-    #        shape=(
-    #            ceil((channel_end - channel_start) / channel_step),
-    #            FILE_TIME_SAMPLE_AMOUNT
-    #        ),
-    #        dtype=NP.int32
-    #    )
-    #    file_handle = open(file_path, 'rb')
-    #    data_index = 0
-    #    for channel_index in range(channel_start, channel_end, channel_step):
-    #        file_handle.seek(channel_index * FILE_TIME_SAMPLE_AMOUNT)
-    #        channel_data = NP.frombuffer(file_handle.read(FILE_TIME_SAMPLE_AMOUNT))
-    #        data[data_index] = channel_data
-    #        data_index += 1
-    #    file_handle.close()
-    #    data = data[:, rel_t_start:rel_t_end:t_step]
-
-    data = NP.fromfile(
-        file_path,
-        dtype = NP.int32,
-        offset = channel_start * FILE_TIME_SAMPLE_AMOUNT * DTYPE_SIZE,
-        count = (channel_end-channel_start) * FILE_TIME_SAMPLE_AMOUNT
-    )
-    data.shape = (channel_end-channel_start, FILE_TIME_SAMPLE_AMOUNT)
-    data = data[::channel_step, rel_t_start:rel_t_end:t_step]
-
-    print("Args (channel):", channel_start, channel_end, channel_step)
-    print("Args (time):", rel_t_start, rel_t_end, rel_t_end)
-    print("Fresh after loading: ", data.shape)
-    data = data.transpose() # Extremely efficient :)
-    return data
-
-def _load_from_h5_X(file_path, rel_t_start, rel_t_end, t_step, channel_start, channel_end, channel_step) -> NP.ndarray:
-    DTYPE_SIZE = 4
-    t1 = time()
-    mm = NP.memmap(file_path, dtype=NP.int32, mode='readonly')
-    mm.shape = (CHANNEL_AMOUNT, FILE_TIME_SAMPLE_AMOUNT)
-    t2 = time()
-    data = mm[channel_start:channel_end:channel_step, rel_t_start:rel_t_end:t_step]
-    t3 = time()
-    data = NP.array(data)
-    t4 = time()
-    data = data.transpose() # Extremely efficient :)
-    t5 = time()
-    print("DELTAS", t2-t1, t3-t2, t4-t3, t5-t4)
-    #print("Args (channel):", channel_start, channel_end, channel_step)
-    #print("Args (time):", rel_t_start, rel_t_end, rel_t_end)
-    #print("Fresh after loading: ", data.shape)
-    return data
-
-FILE_FINDER = FileFinder(DATA_ROOT, ".h5.bin", _filename_to_posix_timestamp)
-
-
-def create_chunk():
-    return Chunk( 
-                FILE_FINDER, 
-                CHANNEL_AMOUNT, 
-                FILE_TIME_SAMPLE_AMOUNT, 
-                True, 
-                8,
-                False,
-                _load_from_h5
-            )

das2numpy-1.1/src/das2numpy/setups/silixa_200hz.py

@@ -1,105 +0,0 @@
-""" Univsersal setup file for silixa, that detects sampling rate and number of channels by itself. 
-The root directory shall be supplied by the user via an argument
-"""
-
-import sys as SYS
-from os import path as P
-import datetime as DT
-import numpy as NP
-from ..filefinder import FileFinder, to_posix_timestamp_ms
-from ..chunk import Chunk
-from .light_tdms_reader import TdmsReader
-from ..utils import bin
-
-CALIBRATE = True
-
-
-
-sample_rate = 200
-
-
-def init(root_path, num_worker_threads):
-    assert P.isdir(root_path)
-    file_finder = FileFinder(root_path, ".tdms", filename_to_posix_timestamp)
-    assert num_worker_threads >= 1
-    multithreaded = num_worker_threads > 1
-    return Chunk(
-                file_finder,
-                sample_rate,
-                multithreaded,
-                num_worker_threads,
-                False,
-                load_file
-            )
-
-
-def filename_to_posix_timestamp(file_name:str) -> int:
-    timestamp_str = file_name.split("_UTC_")[1][:19]
-    timestamp_dt = DT.datetime.strptime(timestamp_str, "%Y%m%d_%H%M%S.%f")
-    timestamp_ms = to_posix_timestamp_ms(timestamp_dt)
-    return timestamp_ms
-
-
-
-def load_file(file_path, file_timestamp, t_start, t_end, t_step, channel_start, channel_end, channel_step) -> NP.ndarray:
-    """ Loads a single file, trims it. And returns the trimmed data as a numpy array. Downsampling (t_step, channel_step) is also possible!
-    """
-    
-    with TdmsReader(file_path) as tdms:
-        data = tdms.get_mmap()
-
-
-        # Trim data
-        idx_start = 0
-        if t_start > file_timestamp: # Check if beginning should be trimmed.
-            rel_t_start = t_start - file_timestamp
-            idx_start = int(rel_t_start * sample_rate / 1000.0)
-        idx_end = data.shape[0] 
-        if t_end < file_timestamp + (data.shape[0] * 1000 / sample_rate): # Check if end should be trimmed
-            rel_t_end = t_end - file_timestamp
-            idx_end = int(rel_t_end * sample_rate / 1000.0) 
-        if idx_start == idx_end:
-            return NP.zeros(shape=[0, 0]) # No data should be loaded. Do nothing
-        if file_timestamp + (data.shape[0] * 1000 / sample_rate) <= t_start:
-            print("Warning: File does not contain any parts of the requested data.",
-                    "This can happen if there are leaks in the data. The corresponding output will be left filled with zeros.\n",
-                    f"    Requested range (Posixtimestamps in ms): [{t_start}, {t_end}[\n",
-                    f"    Filepath: {file_path}.")
-            return NP.zeros(shape=[0, 0])
-        assert idx_end == data.shape[0] or idx_end > idx_start, f"idx_start={idx_start}, idx_end={idx_end}."
-        print(idx_start, idx_end)
-        data = data[idx_start:idx_end, channel_start:channel_end]
-
-
-        # Downsample data
-        if t_step != 1 or channel_step != 1:
-            data = bin(data, (t_step, channel_step))
-        #if t_step != 1:
-        #    data = data[::t_step]
-        #if channel_step != 1:
-        #    data = data[:, ::channel_step]
-        assert len(data) > 0
-
-        if CALIBRATE:
-            data = calibrate(data)
-
-    return data
-
-
-def calibrate(data:NP.ndarray) -> NP.ndarray:
-    """ Convert raw data to strain rate data. 
-    As the resulting values are decimals, the datatype should be float. Otherwise an assertion fails. """
-    #assert data.dtype in (NP.float, NP.float32, NP.float64), f"The data should be floating point. It is {data.dtype}"
-    if data.dtype not in (float, NP.float32, NP.float64):
-        NEW_TYPE = NP.float32
-        #print("Warning: For calibration the data has to be of type float. Converting from {data.dtype} to {NEW_TYPE}")
-        data = data.astype(NEW_TYPE)
-
-    SAMPLE_FREQ = 1000.0 # This remains 1000.0 and not 200 Hz because the original sample rate of the device is relevant here!
-    EICHLAENGE = 10.0
-    factor = 116.0 * 10.0**(-9.0) / 8192.0 * SAMPLE_FREQ / EICHLAENGE
-    return data * factor # Result: 1 / s
-
-
-
-