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Merged
ketiltrout merged 2 commits into from
Jan 31, 2025
Merged

Linting fixes #91

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cebbd8f
chore: Update code for new linter versions
ketiltrout Jan 31, 2025
2ce030a
doc(finder): Update the worked example
ketiltrout Jan 31, 2025
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52 changes: 25 additions & 27 deletions ch_util/_db_tables.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,7 @@ def set_user(u):
# Find the user.
if isinstance(u, int):
q = chimedb.core.proxy.execute_sql(
"SELECT user_id FROM chimewiki.user WHERE user_id = %d;" % u
f"SELECT user_id FROM chimewiki.user WHERE user_id = {u};"
)
else:
q = chimedb.core.proxy.execute_sql(
Expand Down Expand Up @@ -359,7 +359,7 @@ def start(self, time=datetime.datetime.now(), notes=None):
e = event.create(
graph_obj=o, type=event_type.global_flag(), start=start, end=None
)
logger.info("Created global flag as event %d." % e.id)
logger.info(f"Created global flag as event {e.id}.")
return g

def end(self, time=datetime.datetime.now(), notes=None):
Expand Down Expand Up @@ -649,7 +649,7 @@ def add_history(self, notes, time=datetime.datetime.now(), timestamp_notes=None)
h = component_history.create(id=o, comp=self, notes=notes)
t_stamp = timestamp.create(time=time, notes=timestamp_notes)
e = event.create(graph_obj=o, type=event_type.comp_history(), start=t_stamp)
logger.info("Added component history as event %d." % e.id)
logger.info(f"Added component history as event {e.id}.")
return h

def add_doc(self, repo, ref, time=datetime.datetime.now(), notes=None):
Expand Down Expand Up @@ -681,7 +681,7 @@ def add_doc(self, repo, ref, time=datetime.datetime.now(), notes=None):
d = component_doc.create(id=o, comp=self, repo=repo, ref=ref)
t_stamp = timestamp.create(time=time, notes=notes)
e = event.create(graph_obj=o, type=event_type.comp_doc(), start=t_stamp)
logger.info("Added component document as event %d." % e.id)
logger.info(f"Added component document as event {e.id}.")
return d

def get_property(self, type=None, time=datetime.datetime.now()):
Expand Down Expand Up @@ -1216,7 +1216,7 @@ def deactivate(self):
fail = []

if not self.active:
logger.info("Event %d is already deactivated." % (self.id))
logger.info(f"Event {self.id} is already deactivated.")
return

# If this is about component availability, do not deactivate if it is
Expand Down Expand Up @@ -1278,7 +1278,7 @@ def deactivate(self):

self.active = False
self.save()
logger.info("Deactivated event %d." % self.id)
logger.info(f"Deactivated event {self.id}.")

def _replace(self, start=None, end=None, force_end=False):
"""Replace one or both timestamps for an event.
Expand Down Expand Up @@ -1474,7 +1474,7 @@ def _graph_obj_iter(sel, obj, time, when, order, active):
elif order == ORDER_DESC:
ret = ret.order_by(timestamp.time.desc())
else:
raise ValueError("Unknown value of 'when' passed (%d)." % when)
raise ValueError(f"Unknown value of 'when' passed ({when}).")

return ret

Expand Down Expand Up @@ -1668,18 +1668,16 @@ def add_component(comp, time=datetime.datetime.now(), notes=None, force=False):
time, event_type.comp_avail(), EVENT_AFTER, ORDER_ASC
).get()
e_old._replace(start=t_stamp)
logger.debug(
"Added %s by replacing previous event %d." % (comp.sn, e_old.id)
)
logger.debug(f"Added {comp.sn} by replacing previous event {e_old.id}.")
except pw.DoesNotExist:
e = event.create(
graph_obj=comp.id, type=event_type.comp_avail(), start=t_stamp
)
logger.debug("Added %s with new event %d." % (comp.sn, e.id))
logger.debug(f"Added {comp.sn} with new event {e.id}.")
if len(to_add):
logger.info(
"Added %d new component%s: %s"
% (len(to_add), _plural(to_add), ", ".join(to_add_sn))
f"Added {len(to_add)} new component{_plural(to_add)}: "
+ ", ".join(to_add_sn)
)
else:
logger.info("Added no new component.")
Expand Down Expand Up @@ -1823,11 +1821,10 @@ def remove_component(comp, time=datetime.datetime.now(), notes=None, force=False
for e in ev:
e.end = t_stamp
e.save()
logger.debug("Removed component by ending event %d." % e.id)
logger.debug(f"Removed component by ending event {e.id}.")
if len(ev):
logger.info(
"Removed %d component%s: %s."
% (len(ev), _plural(ev), ", ".join(ev_comp_sn))
f"Removed {len(ev)} component{_plural(ev)}: " + ", ".join(ev_comp_sn)
)
else:
logger.info("Removed no component.")
Expand Down Expand Up @@ -1915,8 +1912,9 @@ def set_property(
fail,
force,
PropertyUnchanged,
"The following component%s "
"property does not change" % ("'s" if len(fail) == 1 else "s'"),
"The following component"
+ ("'s" if len(fail) == 1 else "s'")
+ " property does not change",
)

# End any events that need to be ended.
Expand All @@ -1930,8 +1928,9 @@ def set_property(
# If no value was passed, then we are done.
if not value:
logger.info(
"Removed property %s from the following %d component%s: %s."
% (type.name, len(to_end), _plural(to_end), ", ".join(to_end_sn))
f"Removed property {type.name} from the following {len(to_end)} "
+ f"component{_plural(to_end)}: "
+ ", ".join(to_end_sn)
)
return

Expand Down Expand Up @@ -2014,7 +2013,7 @@ def make_connexion(
# starting at this new time.
e_old = c.event(time, EVENT_AFTER, ORDER_ASC).get()
e_old._replace(start=t_stamp)
logger.debug("Added connexion by replacing previous event %d." % e_old.id)
logger.debug(f"Added connexion by replacing previous event {e_old.id}.")
except pw.DoesNotExist:
try:
conn = connexion.from_pair(c.comp1, c.comp2, allow_new=False)
Expand All @@ -2027,11 +2026,11 @@ def make_connexion(
else:
e_type = event_type.connexion()
e = event.create(graph_obj=o, type=e_type, start=t_stamp)
logger.debug("Added connexion with new event %d." % e.id)
logger.debug(f"Added connexion with new event {e.id}.")
if len(to_conn):
logger.info(
"Added %d new connexion%s: %s"
% (len(to_conn), _plural(to_conn), ", ".join(to_conn_sn))
f"Added {len(to_conn)} new connexion{_plural(to_conn)}: "
+ ", ".join(to_conn_sn)
)
else:
logger.info("Added no new connexions.")
Expand Down Expand Up @@ -2109,11 +2108,10 @@ def sever_connexion(conn, time=datetime.datetime.now(), notes=None, force=False)
for e in ev:
e.end = t_stamp
e.save()
logger.debug("Severed connexion by ending event %d." % e.id)
logger.debug(f"Severed connexion by ending event {e.id}.")
if len(ev):
logger.info(
"Severed %d connexion%s: %s."
% (len(ev), _plural(ev), ", ".join(ev_conn_sn))
f"Severed {len(ev)} connexion{_plural(ev)}: " + ", ".join(ev_conn_sn)
)
else:
logger.info("Severed no connexion.")
11 changes: 4 additions & 7 deletions ch_util/andata.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -979,7 +979,7 @@ def _find_mux(self, mux):
for dummy, d in self.datasets.items():
if d.attrs["mux_address"] == mux:
return d
raise ValueError("No dataset with mux = %d is present." % (mux))
raise ValueError(f"No dataset with mux = {mux} is present.")

def chan(self, mux=-1):
"""Convenience access to the list of channels in a given mux.
Expand Down Expand Up @@ -1062,7 +1062,7 @@ def tod(self, chan, mux=-1):
try:
idx = list(self.index_map[chan_map]).index(chan)
except KeyError:
raise ValueError("No channel %d exists for mux %d." % (chan, mux))
raise ValueError(f"No channel {chan} exists for mux {mux}.")

# Return the data.
return ds[idx, :]
Expand Down Expand Up @@ -3381,8 +3381,7 @@ def _remap_crate_corr(afile, slot):
]

# Create new list of serials
serial_pat = crate_serial + ("%02i%%02i" % int(slot))
serials = [serial_pat % ci for ci in chanlist]
serials = [f"{crate_serial}{slot:02}{ci:02}" for ci in chanlist]

# Create a list of channel ids (taking into account that they are
# meaningless for the old crate)
Expand Down Expand Up @@ -3517,9 +3516,7 @@ def _insert_gains(data, input_sel):
elif key in data.history["acq"]:
g_data = data.history["acq"][key]
else:
warnings.warn(
"Cannot find gain entry [%s] for channel %i" % (key, chan)
)
warnings.warn(f"Cannot find gain entry [{key}] for channel {chan}")
continue

# Unpack the gain values and construct the gain array
Expand Down
14 changes: 7 additions & 7 deletions ch_util/cal_utils.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ def parameter_names(self):
parameter_names : np.ndarray[nparam,]
Names of the parameters.
"""
return np.array(["param%d" % p for p in range(self.nparam)], dtype=np.bytes_)
return np.array([f"param{p}" for p in range(self.nparam)], dtype=np.bytes_)

@property
def param_corr(self):
Expand Down Expand Up @@ -753,8 +753,8 @@ def ndofi(self):
def parameter_names(self):
"""Array of strings containing the name of the fit parameters."""
return np.array(
["%s_poly_real_coeff%d" % (self.poly_type, p) for p in range(self.nparr)]
+ ["%s_poly_imag_coeff%d" % (self.poly_type, p) for p in range(self.npari)],
[f"{self.poly_type}_poly_real_coeff{p}" for p in range(self.nparr)]
+ [f"{self.poly_type}_poly_imag_coeff{p}" for p in range(self.npari)],
dtype=np.bytes_,
)

Expand Down Expand Up @@ -1144,8 +1144,8 @@ def ndofp(self):
def parameter_names(self):
"""Array of strings containing the name of the fit parameters."""
return np.array(
["%s_poly_amp_coeff%d" % (self.poly_type, p) for p in range(self.npara)]
+ ["%s_poly_phi_coeff%d" % (self.poly_type, p) for p in range(self.nparp)],
[f"{self.poly_type}_poly_amp_coeff{p}" for p in range(self.npara)]
+ [f"{self.poly_type}_poly_phi_coeff{p}" for p in range(self.nparp)],
dtype=np.bytes_,
)

Expand Down Expand Up @@ -1421,7 +1421,7 @@ def parameter_names(self):
"""Array of strings containing the name of the fit parameters."""
return np.array(
["peak_amplitude", "centroid", "fwhm"]
+ ["%s_poly_phi_coeff%d" % (self.poly_type, p) for p in range(self.nparp)],
+ [f"{self.poly_type}_poly_phi_coeff{p}" for p in range(self.nparp)],
dtype=np.bytes_,
)

Expand Down Expand Up @@ -1695,7 +1695,7 @@ def fit_point_source_map(
absolute_sigma=True,
) # , bounds=bounds)
except ValueError as error:
print("index (" + ", ".join(["%d" % ii for ii in index]) + "):", error)
print("index (" + ", ".join([str(ii) for ii in index]) + "):", error)
continue

# Save the results
Expand Down
78 changes: 37 additions & 41 deletions ch_util/finder.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
import time
import socket
import peewee as pw
import tabulate

import caput.time as ctime

Expand Down Expand Up @@ -144,22 +145,24 @@ class Finder:
>>> from datetime import datetime
>>> f = finder.Finder()
>>> f.only_corr()
>>> f.set_time_range(datetime(2014,02,24), datetime(2014,02,25))
>>> f.set_time_range(datetime(2014,2,24), datetime(2014,2,25))
>>> f.print_results_summary()
interval | acquisition | offset from start (s) | length (s) | N files
1 | 20140219T145849Z_abbot_corr | 378053.1 | 86400.0 | 25
2 | 20140224T051212Z_stone_corr | 0.0 | 67653.9 | 19
Total 154053.858720 seconds of data.
# acquisition start (s) len (s) files MB
--- --------------------------- ----------- --------- ------- -------
0 20140219T145849Z_abbot_corr 378053 86400 25 3166.08
1 20140224T051212Z_stone_corr 0 67653.9 19 2406.78
Total 154054 seconds, 5573 MB of data.

Search for transits of a given source.

>>> import ch_ephem.sources
>>> f.include_transits(ch_ephem.sources.CasA, time_delta=3600)
>>> f.print_results_summary()
interval | acquisition | offset from start (s) | length (s) | N files
1 | 20140219T145849Z_abbot_corr | 452087.2 | 3600.0 | 2
2 | 20140224T051212Z_stone_corr | 55288.0 | 3600.0 | 2
Total 7200.000000 seconds of data.
# acquisition start (s) len (s) files MB
--- --------------------------- ----------- --------- ------- -------
0 20140219T145849Z_abbot_corr 452092 3600 2 253.286
1 20140224T051212Z_stone_corr 55292.9 3600 2 253.346
Total 7200 seconds, 507 MB of data.

To read the data,

Expand All @@ -183,50 +186,45 @@ class Finder:
... & (di.CorrAcqInfo.nprod == 36)
... & (di.ArchiveInst.name == 'stone'))
>>> f.print_results_summary()
interval | acquisition | offset from start (s) | length (s) | N files
1 | 20140211T020307Z_stone_corr | 0.0 | 391.8 | 108
2 | 20140128T135105Z_stone_corr | 0.0 | 4165.2 | 104
3 | 20131208T070336Z_stone_corr | 0.0 | 1429.8 | 377
4 | 20140212T014603Z_stone_corr | 0.0 | 2424.4 | 660
5 | 20131210T060233Z_stone_corr | 0.0 | 1875.3 | 511
6 | 20140210T021023Z_stone_corr | 0.0 | 874.1 | 240
Total 11160.663510 seconds of data.
# acquisition start (s) len (s) files MB
--- --------------------------- ----------- --------- ------- --------
0 20140211T020307Z_stone_corr 0 391.764 108 13594.1
1 20140128T135105Z_stone_corr 0 4165.22 104 131711
2 20131208T070336Z_stone_corr 0 1429.78 377 47676.4
3 20140212T014603Z_stone_corr 0 2424.43 660 83604.1
4 20131210T060233Z_stone_corr 0 1875.32 511 64704.8
5 20140210T021023Z_stone_corr 0 874.144 240 30286.4
Total 11161 seconds, 371577 MB of data.


Here is an example that uses node spoofing and also filters files within
acquisitions to include only LNA housekeeping files:

>>> f = finder.Finder(node_spoof = {"gong" : "/mnt/gong/archive",
"suzu" : "/mnt/suzu/hk_data"})
>>> f = finder.Finder(node_spoof={"scinet_hpss": "/dev/null"})
>>> f.only_hk()
>>> f.set_time_range(datetime(2014, 9, 1), datetime(2014, 10, 10))
>>> f.print_results_summary()
# | acquisition |start (s)| len (s) |files | MB
0 | 20140830T005410Z_ben_hk | 169549 | 419873 | 47 | 2093
1 | 20140905T203905Z_ben_hk | 0 | 16969 | 2 | 0
2 | 20140908T153116Z_ben_hk | 0 | 1116260 | 56 | 4
3 | 20141009T222415Z_ben_hk | 0 | 5745 | 2 | 0
# acquisition start (s) len (s) files MB
--- ----------------------- ----------- ---------------- ------- ------------
0 20140830T005410Z_ben_hk 169549 419873 47 2093
1 20140905T203905Z_ben_hk 0 16969.1 2 0.0832596
2 20140908T153116Z_ben_hk 0 1.11626e+06 56 4.45599
3 20141009T222415Z_ben_hk 0 5744.8 2 0.191574
Total 1558847 seconds, 2098 MB of data.
>>> res = f.get_results(file_condition = (di.HKFileInfo.atmel_name == "LNA"))
>>> for r in res:
... print("No. files: %d" % (len(r[0]))
... print(f"No. files: {len(r[0])}")
...
No. files: 8
No. files: 1
No. files: 19
No. files: 1
>>> data = res[0].as_loaded_data()
>>> for m in data.mux:
... print("Mux %d: %s", (m, data.chan(m)))
Mux 0: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
Mux 1: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
Mux 2: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
>>> print(data.tod(14, 1))
[1744.190917, 1766.344726, 1771.033569, ..., 1928.612792, 1938.900756, 1945.534912]

In the above example, the restriction to LNA housekeeping could also have
been accomplished with the convenience method :meth:`Finder.set_hk_input`:

>>> f.set_hk_input("LNA")
>>> res = f.get_results()

"""

# Constructors and setup
Expand Down Expand Up @@ -1327,17 +1325,14 @@ def print_acq_info(self):
def print_results_summary(self):
"""Print a summary of the search results."""

row_proto = "%4d | %-36s | %7.f | %7.f | %4d | %6.f"
total_data = 0.0
total_size = 0.0
interval_number = 0
titles = ("# ", " acquisition", "start (s)", "len (s) ", "files ", "MB ")
print("%5s|%-38s|%9s|%9s|%6s|%8s" % titles)
titles = ("#", "acquisition", "start (s)", "len (s)", "files", "MB")
rows = []
for ii, acq in enumerate(self.acqs):
acq_start = acq.start_time
intervals = self.get_results_acq(ii)
# if len(intervals):
# print intervals[0]
for interval in intervals:
offset = interval[1][0] - acq_start
length = interval[1][1] - interval[1][0]
Expand Down Expand Up @@ -1366,11 +1361,12 @@ def print_results_summary(self):
except TypeError:
s = 0
info = (interval_number, acq.name, offset, length, n_files, s)
print(row_proto % info)
rows.append(info)
total_data += length
total_size += s
interval_number += 1
print(f"Total {total_data:6.f} seconds, {total_size:6.f} MB of data.")
print(tabulate.tabulate(rows, headers=titles))
print(f"Total {total_data:6.0f} seconds, {total_size:6.0f} MB of data.")


def _trim_intervals_range(intervals, time_range, min_interval=0.0):
Expand Down
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