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Add support for EC-Lab v11.50 (rebased) #97

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merged 5 commits into from
Feb 6, 2024
Merged

Add support for EC-Lab v11.50 (rebased) #97

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77d5629
Added support for v11.50 :
JhonFlash3008 Jan 20, 2024
46f296f
Merge branch 'master' into JhonFlash-master
chatcannon Feb 3, 2024
7a6ac1c
added tests for v11.50
JhonFlash3008 Jan 22, 2024
5cdc620
Fix flake8 lint
chatcannon Feb 3, 2024
4971f2b
Apply review comments
chatcannon Feb 3, 2024
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87 changes: 71 additions & 16 deletions galvani/BioLogic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,7 @@ def fieldname_to_dtype(fieldname):
"/F",
"/mF",
"/uF",
"/µF",
"/C",
"/Ohm",
)
Expand Down Expand Up @@ -230,7 +231,7 @@ def MPTfileCSV(file_or_path):
return mpt_csv, comments


VMPmodule_hdr = np.dtype(
VMPmodule_hdr_v1 = np.dtype(
[
("shortname", "S10"),
("longname", "S25"),
Expand All @@ -240,15 +241,27 @@ def MPTfileCSV(file_or_path):
]
)

VMPmodule_hdr_v2 = np.dtype(
[
("shortname", "S10"),
("longname", "S25"),
("max points", "<u4"),
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("length", "<u4"),
("version", "<u4"),
("unknown2", "<u4"),
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("date", "S8"),
]
)

# Maps from colID to a tuple defining a numpy dtype
VMPdata_colID_dtype_map = {
4: ("time/s", "<f8"),
5: ("control/V/mA", "<f4"),
6: ("Ewe/V", "<f4"),
7: ("dQ/mA.h", "<f8"),
7: ("dq/mA.h", "<f8"),
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8: ("I/mA", "<f4"), # 8 is either I or <I> ??
9: ("Ece/V", "<f4"),
11: ("I/mA", "<f8"),
11: ("<I>/mA", "<f8"),
13: ("(Q-Qo)/mA.h", "<f8"),
16: ("Analog IN 1/V", "<f4"),
19: ("control/V", "<f4"),
Expand All @@ -266,7 +279,7 @@ def MPTfileCSV(file_or_path):
39: ("I Range", "<u2"),
69: ("R/Ohm", "<f4"),
70: ("P/W", "<f4"),
74: ("Energy/W.h", "<f8"),
74: ("|Energy|/W.h", "<f8"),
75: ("Analog OUT/V", "<f4"),
76: ("<I>/mA", "<f4"),
77: ("<Ewe>/V", "<f4"),
Expand All @@ -286,8 +299,30 @@ def MPTfileCSV(file_or_path):
169: ("Cs/µF", "<f4"),
172: ("Cp/µF", "<f4"),
173: ("Cp-2/µF-2", "<f4"),
174: ("Ewe/V", "<f4"),
241: ("|E1|/V", "<f4"),
174: ("<Ewe>/V", "<f4"),
178: ("(Q-Qo)/C", "<f4"),
179: ("dQ/C", "<f4"),
211: ("Q charge/discharge/mA.h", "<f8"),
212: ("half cycle", "<u4"),
213: ("z cycle", "<u4"),
217: ("THD Ewe/%", "<f4"),
218: ("THD I/%", "<f4"),
220: ("NSD Ewe/%", "<f4"),
221: ("NSD I/%", "<f4"),
223: ("NSR Ewe/%", "<f4"),
224: ("NSR I/%", "<f4"),
230: ("|Ewe h2|/V", "<f4"),
231: ("|Ewe h3|/V", "<f4"),
232: ("|Ewe h4|/V", "<f4"),
233: ("|Ewe h5|/V", "<f4"),
234: ("|Ewe h6|/V", "<f4"),
235: ("|Ewe h7|/V", "<f4"),
236: ("|I h2|/A", "<f4"),
237: ("|I h3|/A", "<f4"),
238: ("|I h4|/A", "<f4"),
239: ("|I h5|/A", "<f4"),
240: ("|I h6|/A", "<f4"),
241: ("|I h7|/A", "<f4"),
242: ("|E2|/V", "<f4"),
271: ("Phase(Z1) / deg", "<f4"),
272: ("Phase(Z2) / deg", "<f4"),
Expand Down Expand Up @@ -440,11 +475,18 @@ def read_VMP_modules(fileobj, read_module_data=True):
raise ValueError(
"Found %r, expecting start of new VMP MODULE" % module_magic
)
VMPmodule_hdr = VMPmodule_hdr_v1

# Reading headers binary information
hdr_bytes = fileobj.read(VMPmodule_hdr.itemsize)
if len(hdr_bytes) < VMPmodule_hdr.itemsize:
raise IOError("Unexpected end of file while reading module header")

# Checking if EC-Lab version is >= 11.50
if hdr_bytes[35:39] == b"\xff\xff\xff\xff":
VMPmodule_hdr = VMPmodule_hdr_v2
hdr_bytes += fileobj.read(VMPmodule_hdr_v2.itemsize - VMPmodule_hdr_v1.itemsize)

hdr = np.frombuffer(hdr_bytes, dtype=VMPmodule_hdr, count=1)
hdr_dict = dict(((n, hdr[n][0]) for n in VMPmodule_hdr.names))
hdr_dict["offset"] = fileobj.tell()
Expand All @@ -456,7 +498,11 @@ def read_VMP_modules(fileobj, read_module_data=True):
current module: %s
length read: %d
length expected: %d"""
% (hdr_dict["longname"], len(hdr_dict["data"]), hdr_dict["length"])
% (
hdr_dict["longname"],
len(hdr_dict["data"]),
hdr_dict["length"],
)
)
yield hdr_dict
else:
Expand Down Expand Up @@ -494,6 +540,8 @@ def __init__(self, file_or_path):
raise ValueError("Invalid magic for .mpr file: %s" % magic)

modules = list(read_VMP_modules(mpr_file))
mpr_file.close() # close the mpr.file after reading all of it
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self.modules = modules
(settings_mod,) = (m for m in modules if m["shortname"] == b"VMP Set ")
(data_module,) = (m for m in modules if m["shortname"] == b"VMP data ")
Expand All @@ -504,15 +552,22 @@ def __init__(self, file_or_path):
n_columns = np.frombuffer(data_module["data"][4:5], dtype="u1").item()

if data_module["version"] == 0:
column_types = np.frombuffer(
data_module["data"][5:], dtype="u1", count=n_columns
)
remaining_headers = data_module["data"][5 + n_columns:100]
main_data = data_module["data"][100:]
# If EC-Lab version >= 11.50, column_types is [0 1 0 3 0 174...] instead of [1 3 174...]
if np.frombuffer(data_module["data"][5:6], dtype="u1").item():
column_types = np.frombuffer(data_module["data"][5:], dtype="u1", count=n_columns)
remaining_headers = data_module["data"][5 + n_columns:100]
main_data = data_module["data"][100:]
else:
column_types = np.frombuffer(
data_module["data"][5:], dtype="u1", count=n_columns * 2
)
column_types = column_types[1::2] # suppressing zeros in column types array
# remaining headers should be empty except for bytes 5 + n_columns * 2
# and 1006 which are sometimes == 1
remaining_headers = data_module["data"][6 + n_columns * 2:1006]
main_data = data_module["data"][1007:]
elif data_module["version"] in [2, 3]:
column_types = np.frombuffer(
data_module["data"][5:], dtype="<u2", count=n_columns
)
column_types = np.frombuffer(data_module["data"][5:], dtype="<u2", count=n_columns)
# There are bytes of data before the main array starts
if data_module["version"] == 3:
num_bytes_before = 406 # version 3 added `\x01` to the start
Expand Down Expand Up @@ -541,7 +596,7 @@ def __init__(self, file_or_path):
if maybe_loop_module:
(loop_module,) = maybe_loop_module
if loop_module["version"] == 0:
self.loop_index = np.fromstring(loop_module["data"][4:], dtype="<u4")
self.loop_index = np.frombuffer(loop_module["data"][4:], dtype="<u4")
self.loop_index = np.trim_zeros(self.loop_index, "b")
else:
raise ValueError(
Expand Down