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plot saving to be specified in config.user #157

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28dff4e
plot saving to be specified in config.user
nataliejpg Dec 5, 2018
af2bf27
make requirement for config.user section to be flatter
nataliejpg Dec 5, 2018
d47932b
remove plottr import from doNd example notebook
nataliejpg Dec 5, 2018
000a399
make save_image more flexible so that it can be used outside of the d…
nataliejpg Apr 8, 2019
5cbebbb
fix bugs where old private function name used and name extension adde…
nataliejpg Apr 8, 2019
26024f0
Merge branch 'master' into plot_saving_to_config
nataliejpg Apr 8, 2019
66679ce
change kwarg experiment_name to shorter (and used elsewhere) exp_name…
nataliejpg Apr 9, 2019
25f38d1
resetting doND example to master version
nataliejpg Apr 13, 2019
1103d53
run example notebook to check i didnt break anything and make plottr …
nataliejpg Apr 13, 2019
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71 changes: 41 additions & 30 deletions examples/dataset/Example of doND wrappers.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -24,7 +24,10 @@
"from qcodes.dataset.database import initialise_database\n",
"from qcodes.dataset.experiment_container import new_experiment\n",
"from qcodes.dataset.plotting import plot_by_id\n",
"import plottr\n",
"try:\n",
" import plottr\n",
"except ModuleNotFoundError:\n",
" pass\n",
"import qcodes.config\n",
"from qcodes.tests.instrument_mocks import DummyChannelInstrument"
]
Expand All @@ -46,17 +49,25 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Upgrading database: : 0it [00:00, ?it/s]\n",
"Upgrading database: : 0it [00:00, ?it/s]\n"
]
},
{
"data": {
"text/plain": [
"doNd-tutorial#no sample#10@C:\\Users\\jenielse/experiments.db\n",
"-----------------------------------------------------------"
"doNd-tutorial#no sample#1@/Users/natalie/experiments.db\n",
"-------------------------------------------------------"
]
},
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -68,7 +79,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -81,7 +92,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -100,7 +111,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -120,15 +131,15 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 27\n",
"plot by id took 0.19638419151306152\n"
"Starting experimental run with id: 1\n",
"plot by id took 0.037342071533203125\n"
]
}
],
Expand All @@ -138,7 +149,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"metadata": {
"scrolled": false
},
Expand All @@ -147,8 +158,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 28\n",
"plot by id took 1.528921365737915\n"
"Starting experimental run with id: 2\n",
"plot by id took 0.3784291744232178\n"
]
}
],
Expand All @@ -175,7 +186,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -197,15 +208,15 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"called before the loop\n",
"Starting experimental run with id: 29\n",
"Starting experimental run with id: 6\n",
"called at each step\n",
"called at each step\n",
"called at each step\n",
Expand All @@ -217,7 +228,7 @@
"called at each step\n",
"called at each step\n",
"called after the loop\n",
"plot by id took 0.1400294303894043\n"
"plot by id took 0.03285670280456543\n"
]
}
],
Expand All @@ -228,15 +239,15 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"called before the loop\n",
"Starting experimental run with id: 30\n",
"Starting experimental run with id: 7\n",
"called before inner loop\n",
"called at each step\n",
"called at each step\n",
Expand All @@ -250,7 +261,7 @@
"called at each step\n",
"called after inner loop\n",
"called after the loop\n",
"plot by id took 0.18652963638305664\n"
"plot by id took 0.06169295310974121\n"
]
}
],
Expand All @@ -272,7 +283,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -281,15 +292,15 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 31\n",
"plot by id took 0.15599322319030762\n"
"Starting experimental run with id: 8\n",
"plot by id took 0.03528785705566406\n"
]
}
],
Expand Down Expand Up @@ -328,7 +339,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -337,15 +348,15 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting experimental run with id: 35\n",
"plot by id took 0.07499814033508301\n"
"Starting experimental run with id: 9\n",
"plot by id took 0.045063018798828125\n"
]
}
],
Expand Down
87 changes: 56 additions & 31 deletions qdev_wrappers/dataset/doNd.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,21 @@ def do0d(*param_meas: Union[_BaseParameter, Callable[[], None]],
dataid = datasaver.run_id

if do_plot is True:
ax, cbs = _save_image(datasaver)
plt.ioff()
start = time.time()
axes, cbs = plot_by_id(dataid)
stop = time.time()
print(f"plot by id took {stop-start}")
plt.ion()
exp_name = datasaver._dataset.exp_name
sample_name = datasaver._dataset.sample_name
save_image(axes, exp_name=exp_name,
sample_name=sample_name, run_id=dataid)
else:
ax = None,
axes = None,
cbs = None

return dataid, ax, cbs
return dataid, axes, cbs


def do1d(param_set: _BaseParameter, start: number, stop: number,
Expand Down Expand Up @@ -136,14 +145,23 @@ def do1d(param_set: _BaseParameter, start: number, stop: number,
dataid = datasaver.run_id # convenient to have for plotting

if do_plot is True:
ax, cbs = _save_image(datasaver)
plt.ioff()
start = time.time()
axes, cbs = plot_by_id(dataid)
stop = time.time()
print(f"plot by id took {stop-start}")
plt.ion()
exp_name = datasaver._dataset.exp_name
sample_name = datasaver._dataset.sample_name
save_image(axes, exp_name=exp_name,
sample_name=sample_name, run_id=dataid)
else:
ax = None,
axes = None,
cbs = None

if interrupted:
raise KeyboardInterrupt
return dataid, ax, cbs
return dataid, axes, cbs


def do2d(param_set1: _BaseParameter, start1: number, stop1: number,
Expand Down Expand Up @@ -235,17 +253,27 @@ def do2d(param_set1: _BaseParameter, start1: number, stop1: number,
dataid = datasaver.run_id

if do_plot is True:
ax, cbs = _save_image(datasaver)
plt.ioff()
start = time.time()
axes, cbs = plot_by_id(dataid)
stop = time.time()
print(f"plot by id took {stop-start}")
plt.ion()
exp_name = datasaver._dataset.exp_name
sample_name = datasaver._dataset.sample_name
save_image(axes, exp_name=exp_name,
sample_name=sample_name, run_id=dataid)
else:
ax = None,
axes = None,
cbs = None
if interrupted:
raise KeyboardInterrupt

return dataid, ax, cbs
return dataid, axes, cbs


def _save_image(datasaver) -> AxesTupleList:
def save_image(axes, exp_name=None, sample_name=None,
run_id=None, name_extension=None, **kwargs) -> AxesTupleList:
"""
Save the plots created by datasaver as pdf and png

Expand All @@ -254,35 +282,32 @@ def _save_image(datasaver) -> AxesTupleList:
as plot.

"""
plt.ioff()
dataid = datasaver.run_id
start = time.time()
axes, cbs = plot_by_id(dataid)
stop = time.time()
print(f"plot by id took {stop-start}")

run_id = run_id or 0
mainfolder = config.user.mainfolder
experiment_name = datasaver._dataset.exp_name
sample_name = datasaver._dataset.sample_name

storage_dir = os.path.join(mainfolder, experiment_name, sample_name)
os.makedirs(storage_dir, exist_ok=True)

png_dir = os.path.join(storage_dir, 'png')
pdf_dif = os.path.join(storage_dir, 'pdf')
if exp_name and sample_name:
storage_dir = os.path.join(mainfolder, exp_name, sample_name)
os.makedirs(storage_dir, exist_ok=True)
png_dir = os.path.join(storage_dir, 'png')
pdf_dir = os.path.join(storage_dir, 'pdf')
else:
png_dir = 'png'
pdf_dir = 'pdf'

os.makedirs(png_dir, exist_ok=True)
os.makedirs(pdf_dif, exist_ok=True)
os.makedirs(pdf_dir, exist_ok=True)

save_pdf = True
save_png = True
save_pdf = config.user.get('save_pdf', True)
save_png = config.user.get('save_png', True)

for i, ax in enumerate(axes):
filename = f'{run_id}'
if name_extension is not None:
filename += '_' + name_extension
filename += f'_{i}'
if save_pdf:
full_path = os.path.join(pdf_dif, f'{dataid}_{i}.pdf')
full_path = os.path.join(pdf_dir, filename + '.pdf')
ax.figure.savefig(full_path, dpi=500)
if save_png:
full_path = os.path.join(png_dir, f'{dataid}_{i}.png')
full_path = os.path.join(png_dir, filename + '.png')
ax.figure.savefig(full_path, dpi=500)
plt.ion()
return axes, cbs