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Adds dev-cfg defaults for bias_steps and take_bgmap #404

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Adds dev-cfg defaults for bias_steps and take_bgmap #404

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2 changes: 2 additions & 0 deletions sodetlib/det_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,8 @@ def odict_rep(dumper, data):

# Dict of device-specific default params to use for take_iv
'iv_defaults': {},
'take_bgmap_defaults': {},
'take_bias_step_defaults': {},

# Amp stuff
"amps_to_bias": ['hemt', 'hemt1', 'hemt2', '50k', '50k1', '50k2'],
Expand Down
163 changes: 95 additions & 68 deletions sodetlib/operations/bias_steps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,9 @@
import matplotlib.pyplot as plt
import scipy.optimize
from sodetlib.operations import iv
from dataclasses import dataclass, asdict, fields
from typing import Optional
from copy import deepcopy

np.seterr(all='ignore')

Expand Down Expand Up @@ -996,13 +999,58 @@ def plot_Rfrac(bsa, text_loc=(0.6, 0.8)):
transform=ax.transAxes)
return fig, ax

@dataclass
class BiasStepConfig:
bgs: Optional[float] = None
step_voltage: float = 0.05 # Volts (LCM)
step_duration: float = 0.05 # Sec
nsteps: int = 20
high_current_mode: bool = True
hcm_wait_time: float = 3.0
run_analysis: bool = True
analysis_kwargs: Optional[dict] = None
dacs: str = 'pos'
use_waveform: bool = True
channel_mask: Optional[np.ndarray] = None
g3_tag: Optional[str] = None
stream_subtype: str = 'bias_steps'
enable_compression: bool = False
plot_rfrac: bool = True
show_plots: bool = False

def __post_init__(self):
if self.analysis_kwargs is None:
self.analysis_kwargs = {}

if self.dacs not in ['pos', 'neg', 'both']:
raise ValueError(f'dacs={self.dacs} not in ["pos", "neg", "both"]')

@dataclass
class BgmapConfig(BiasStepConfig):
dc_voltage: float = 0.3
step_voltage: float = 0.01
stream_subtype: str = 'bgmap'

def __post_init__(self):
super().__post_init__()

# Makes sure these kwargs are set by default unless otherwise
# specified
kw = {
'assignment_thresh': 0.3, 'create_bgmap': True,
'save_bg_map': True
}
kw.update(self.analysis_kwargs)
self.analysis_kwargs = kw

def get_bias_step_cfg(self):
return BiasStepConfig(
**{f.name: getattr(self, f.name) for f in fields(BiasStepConfig)}
)


@sdl.set_action()
def take_bgmap(S, cfg, bgs=None, dc_voltage=0.3, step_voltage=0.01,
step_duration=0.05, nsteps=20, high_current_mode=True,
hcm_wait_time=0, analysis_kwargs=None, dacs='pos',
use_waveform=True, show_plots=True, g3_tag=None,
enable_compression=False, plot_rfrac=False):
def take_bgmap(S, cfg, **bgmap_pars):
"""
Function to easily create a bgmap. This will set all bias group voltages
to 0 (since this is best for generating the bg map), and run bias-steps
Expand Down Expand Up @@ -1055,51 +1103,34 @@ def take_bgmap(S, cfg, bgs=None, dc_voltage=0.3, step_voltage=0.01,
show_plots : bool
Show plot in addition to saving when running interactively. Default is False.
"""
if bgs is None:
bgs = cfg.dev.exp['active_bgs']
bgs = np.atleast_1d(bgs)
kw = deepcopy(cfg.dev.exp['take_bgmap_defaults'])
kw.update(bgmap_pars)
bgmap_cfg = BgmapConfig(**kw)

if analysis_kwargs is None:
analysis_kwargs = {}
if bgmap_cfg.bgs is None:
bgmap_cfg.bgs = cfg.dev.exp['active_bgs']
bgmap_cfg.bgs = np.atleast_1d(bgmap_cfg.bgs)

for bg in bgs:
S.set_tes_bias_bipolar(bg, dc_voltage)

_analysis_kwargs = {
'assignment_thresh': 0.3,
'create_bg_map': True, 'save_bg_map': True
}
_analysis_kwargs.update(analysis_kwargs)
bsa = take_bias_steps(
S, cfg, bgs, step_voltage=step_voltage, step_duration=step_duration,
nsteps=nsteps, high_current_mode=high_current_mode,
hcm_wait_time=hcm_wait_time, run_analysis=True, dacs=dacs,
use_waveform=use_waveform, g3_tag=g3_tag, stream_subtype='bgmap',
plot_rfrac=plot_rfrac, show_plots=show_plots,
enable_compression=enable_compression, analysis_kwargs=_analysis_kwargs
)
for bg in bgmap_cfg.bgs:
S.set_tes_bias_bipolar(bg, bgmap_cfg.dc_voltage)

bsa = take_bias_steps(S, cfg, **asdict(bgmap_cfg.get_bias_step_cfg()))

if hasattr(bsa, 'bgmap'):
fig, ax = plot_bg_assignment(bsa)
sdl.save_fig(S, fig, 'bg_assignments.png')
if show_plots:
if bgmap_cfg.show_plots:
plt.show()
else:
plt.close()

for bg in bgs:
for bg in bgmap_cfg.bgs:
S.set_tes_bias_bipolar(bg, 0.)

return bsa


@sdl.set_action()
def take_bias_steps(S, cfg, bgs=None, step_voltage=0.05, step_duration=0.05,
nsteps=20, high_current_mode=True, hcm_wait_time=3,
run_analysis=True, analysis_kwargs=None, dacs='pos',
use_waveform=True, channel_mask=None, g3_tag=None,
stream_subtype='bias_steps', enable_compression=False,
plot_rfrac=True, show_plots=False):
def take_bias_steps(S, cfg, **bscfg_pars):
"""
Takes bias step data at the current DC voltage. Assumes bias lines
are already in low-current mode (if they are in high-current this will
Expand Down Expand Up @@ -1160,56 +1191,52 @@ def take_bias_steps(S, cfg, bgs=None, step_voltage=0.05, step_duration=0.05,
show_plots : bool
Show plot in addition to saving when running interactively. Default is False.
"""
if bgs is None:
bgs = cfg.dev.exp['active_bgs']
bgs = np.atleast_1d(bgs)
kw = deepcopy(cfg.dev.exp['take_bias_step_defaults'])
kw.update(bscfg_pars)
bscfg = BiasStepConfig(**kw)

if bscfg.bgs is None:
bscfg.bgs = cfg.dev.exp['active_bgs']
bscfg.bgs = np.atleast_1d(bscfg.bgs)

# Adds to account for steps that may be cut in analysis
nsteps += 4

# Dumb way to get all run kwargs, but we probably want to save these in
# data object
run_kwargs = {
'bgs': bgs, 'step_voltage': step_voltage,
'step_duration': step_duration, 'nsteps': nsteps,
'high_current_mode': high_current_mode,
'hcm_wait_time': hcm_wait_time, 'run_analysis': run_analysis,
'analysis_kwargs': analysis_kwargs, 'channel_mask': channel_mask,
}
bscfg.nsteps += 4

run_kwargs = asdict(bscfg)

initial_ds_factor = S.get_downsample_factor()
initial_filter_disable = S.get_filter_disable()
initial_dc_biases = S.get_tes_bias_bipolar_array()
init_current_mode = sdl.get_current_mode_array(S)

try:
dc_biases = initial_dc_biases
init_current_mode = sdl.get_current_mode_array(S)
if high_current_mode:
if bscfg.high_current_mode:
dc_biases = dc_biases / S.high_low_current_ratio
step_voltage /= S.high_low_current_ratio
sdl.set_current_mode(S, bgs, 1)
S.log(f"Waiting {hcm_wait_time} sec after switching to hcm")
time.sleep(hcm_wait_time)
bscfg.step_voltage /= S.high_low_current_ratio
sdl.set_current_mode(S, bscfg.bgs, 1)
S.log(f"Waiting {bscfg.hcm_wait_time} sec after switching to hcm")
time.sleep(bscfg.hcm_wait_time)

bsa = BiasStepAnalysis(S, cfg, bgs, run_kwargs=run_kwargs)
bsa = BiasStepAnalysis(S, cfg, bscfg.bgs, run_kwargs=run_kwargs)

bsa.sid = sdl.stream_g3_on(
S, tag=g3_tag, channel_mask=channel_mask, downsample_factor=1,
filter_disable=True, subtype=stream_subtype, enable_compression=enable_compression
S, tag=bscfg.g3_tag, channel_mask=bscfg.channel_mask, downsample_factor=1,
filter_disable=True, subtype=bscfg.stream_subtype, enable_compression=bscfg.enable_compression
)

bsa.start = time.time()

for bg in bgs:
if use_waveform:
for bg in bscfg.bgs:
if bscfg.use_waveform:
play_bias_steps_waveform(
S, cfg, bg, step_duration, step_voltage,
num_steps=nsteps
S, cfg, bg, bscfg.step_duration, bscfg.step_voltage,
num_steps=bscfg.nsteps
)
else:
play_bias_steps_dc(
S, cfg, bg, step_duration, step_voltage,
num_steps=nsteps, dacs=dacs,
S, cfg, bg, bscfg.step_duration, bscfg.step_voltage,
num_steps=bscfg.nsteps, dacs=bscfg.dacs,
)
bsa.stop = time.time()

Expand All @@ -1223,18 +1250,18 @@ def take_bias_steps(S, cfg, bgs=None, step_voltage=0.05, step_duration=0.05,
S.set_downsample_factor(initial_ds_factor)
S.set_filter_disable(initial_filter_disable)

if run_analysis:
if bscfg.run_analysis:
S.log("Running bias step analysis")
try:
if analysis_kwargs is None:
if bscfg.analysis_kwargs is None:
analysis_kwargs = {}
bsa.run_analysis(save=True, **analysis_kwargs)
if plot_rfrac:
if bscfg.plot_rfrac:
fig, ax = plot_Rfrac(bsa)
path = sdl.make_filename(S, 'bs_rfrac_summary.png', plot=True)
fig.savefig(path)
S.pub.register_file(path, 'bs_rfrac_summary', plot=True, format='png')
if not show_plots:
if not bscfg.show_plots:
plt.close(fig)
except Exception:
print(f"Bias step analysis failed with exception:")
Expand Down