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Msg replacement #95

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Merged
dihm merged 2 commits into from
Dec 7, 2021
Merged

Msg replacement #95

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fa9eedb
Replace deprecated msgpack with python's pickle for saving dataframes.
dihm Dec 3, 2021
915cc1c
Adding the extra bugfixes found in #91.
dihm Dec 3, 2021
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31 changes: 25 additions & 6 deletions lyse/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
import time
import traceback
import queue
import warnings

# 3rd party imports:
splash.update_text('importing numpy')
Expand All @@ -41,6 +42,7 @@
from labscript_utils.qtwidgets.headerview_with_widgets import HorizontalHeaderViewWithWidgets
from labscript_utils.qtwidgets.outputbox import OutputBox
import labscript_utils.shared_drive as shared_drive
from labscript_utils import dedent

from lyse.dataframe_utilities import (concat_with_padding,
get_dataframe_from_shot,
Expand Down Expand Up @@ -1604,6 +1606,8 @@ def add_files(self, filepaths, new_row_data, done=False):
# Update the Qt model:
for filepath in to_add:
self.update_row(filepath, dataframe_already_updated=True)

app.filebox.set_add_shots_progress(None, None, None)


@inmain_decorator()
Expand Down Expand Up @@ -2245,23 +2249,23 @@ def on_save_dataframe_triggered(self, choose_folder=True):
for sequence in sequences:
sequence_df = pandas.DataFrame(df[df['sequence'] == sequence], columns=df.columns).dropna(axis=1, how='all')
labscript = sequence_df['labscript'].iloc[0]
filename = "dataframe_{}_{}.msg".format(sequence.to_pydatetime().strftime("%Y%m%dT%H%M%S"),labscript[:-3])
filename = "dataframe_{}_{}.pkl".format(sequence.to_pydatetime().strftime("%Y%m%dT%H%M%S"),labscript[:-3])
if not choose_folder:
save_path = os.path.dirname(sequence_df['filepath'].iloc[0])
sequence_df.infer_objects()
for col in sequence_df.columns :
if sequence_df[col].dtype == object:
sequence_df[col] = pandas.to_numeric(sequence_df[col], errors='ignore')
sequence_df.to_msgpack(os.path.join(save_path, filename))
sequence_df.to_pickle(os.path.join(save_path, filename))
else:
error_dialog('Dataframe is empty')

def on_load_dataframe_triggered(self):
default = os.path.join(self.exp_config.get('paths', 'experiment_shot_storage'), 'dataframe.msg')
default = os.path.join(self.exp_config.get('paths', 'experiment_shot_storage'), 'dataframe.pkl')
file = QtWidgets.QFileDialog.getOpenFileName(self.ui,
'Select dataframe file to load',
default,
"dataframe files (*.msg)")
"dataframe files (*.pkl *.msg)")
if type(file) is tuple:
file, _ = file
if not file:
Expand All @@ -2270,7 +2274,22 @@ def on_load_dataframe_triggered(self):
# Convert to standard platform specific path, otherwise Qt likes
# forward slashes:
file = os.path.abspath(file)
df = pandas.read_msgpack(file).sort_values("run time").reset_index()
if file.endswith('.msg'):
# try to read msgpack in case using older pandas
try:
df = pandas.read_msgpack(file).sort_values("run time").reset_index()
# raise a deprecation warning if this succeeds
msg = """msgpack support is being dropped by pandas >= 1.0.0.
Please resave this dataframe to use the new format."""
warnings.warn(dedent(msg),DeprecationWarning)
except AttributeError as err:
# using newer pandas that can't read msg
msg = """msgpack is no longer supported by pandas.
To read this dataframe, you must downgrade pandas to < 1.0.0.
You can then read this dataframe and resave it with the new format."""
raise DeprecationWarning(dedent(msg)) from err
else:
df = pandas.read_pickle(file).sort_values("run time").reset_index()

# Check for changes in the shot files since the dataframe was exported
def changed_since(filepath, time):
Expand All @@ -2281,7 +2300,7 @@ def changed_since(filepath, time):

filepaths = df["filepath"].tolist()
changetime_cache = os.path.getmtime(file)
need_updating = np.where(map(lambda x: changed_since(x, changetime_cache), filepaths))[0]
need_updating = np.where(list(map(lambda x: changed_since(x, changetime_cache), filepaths)))[0]
need_updating = np.sort(need_updating)[::-1] # sort in descending order to not remove the wrong items with pop

# Reload the files where changes where made since exporting
Expand Down