def toggleValue(self, event):
df = self.nmrproblem.df
patoms = self.nmrproblem.protonAtoms
catoms = self.nmrproblem.carbonAtoms
if ipysheet.to_dataframe(self.sheet1).shape == (0, 0):
return
if event.name == 'value':
self.old = event.old
self.new = event.new
# update backend dataframe
# i
if event.old == 'All':
df.loc[:, :] = ipysheet.to_dataframe(self.sheet1).loc[:, :]
elif event.old == 'COSY':
rr = ['ppm'] + patoms
cc = ['ppm'] + patoms
df.loc[rr, cc] = ipysheet.to_dataframe(self.sheet1).loc[rr, cc]
elif event.old == 'HSQC-HMBC':
rr = ['ppm'] + catoms
cc = ['ppm'] + patoms
df.loc[rr, cc] = ipysheet.to_dataframe(self.sheet1).loc[rr, cc]
elif event.old == 'integrals-ppm':
rr = ['ppm', 'integral']
cc = patoms + catoms
df.loc[rr, cc] = ipysheet.to_dataframe(self.sheet1).loc[rr, cc]
df.loc[cc, 'ppm'] = df.loc['ppm', cc]
# update sheet1 display of dataframe
if event.new == 'All':
self.sheet1 = ipysheet.from_dataframe(df)
elif event.new == 'COSY':
rr = ['ppm'] + patoms[::-1]
cc = ['ppm'] + patoms
self.sheet1 = ipysheet.from_dataframe(df.loc[rr, cc])
elif event.new == 'HSQC-HMBC':
rr = ['ppm'] + catoms[::-1]
cc = ['ppm'] + patoms
self.sheet1 = ipysheet.from_dataframe(df.loc[rr, cc])
elif event.new == 'integrals-ppm':
rr = ['ppm', 'integral']
cc = patoms + catoms
self.sheet1 = ipysheet.from_dataframe(df.loc[rr, cc])
self.dfLayout.children = [
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
]
def _df_to_sheet(df: pd.DataFrame) -> sh.Sheet:
"""
Transforms a pandas DataFrame into a ipysheet Sheet.
The cells are set to read only except for the values.
:param df: the pandas DataFrame to be converted
:return the equivalent ipysheet Sheet
"""
if not df.empty:
sheet = sh.from_dataframe(df)
column = df.columns.get_loc("Value")
for cell in sheet.cells:
if column not in (cell.column_start, cell.column_end):
cell.read_only = True
else:
cell.type = "numeric"
# TODO: make the number of decimals depend on the module ?
# or chosen in the ui by the user
cell.numeric_format = "0.000"
# Name, Value, Unit, Description
sheet.column_width = [150, 50, 20, 150]
else:
sheet = sh.sheet()
return sheet
def test_from_dataframe():
df = pd.DataFrame({
'A': 1.,
'B': pd.Timestamp('20130102'),
'C': pd.Series(1, index=list(range(4)), dtype='float32'),
'D': np.array([False, True, False, False], dtype='bool'),
'S': pd.Categorical(["test", "train", "test", "train"]),
'T': 'foo',
'X': np.array([0, 3, 9, 18])
})
df.loc[[0, 2], ['B']] = np.nan
sheet = ipysheet.from_dataframe(df)
assert len(sheet.cells) == 7
assert sheet.cells[0].value == [1., 1., 1., 1.]
assert sheet.cells[0].type == 'numeric'
assert sheet.cells[1].value == [None, '2013/01/02', None, '2013/01/02']
assert sheet.cells[1].type == 'date'
assert sheet.cells[2].value == [1., 1., 1., 1.]
assert sheet.cells[2].type == 'numeric'
assert sheet.cells[2].numeric_format == '0.000'
assert sheet.cells[3].value == [False, True, False, False]
assert sheet.cells[3].type == 'checkbox'
assert sheet.cells[4].value == ['test', 'train', 'test', 'train']
assert sheet.cells[4].type == 'text'
assert sheet.cells[5].value == ['foo', 'foo', 'foo', 'foo']
assert sheet.cells[5].type == 'text'
assert sheet.cells[6].value == [0, 3, 9, 18]
assert sheet.cells[6].type == 'numeric'
assert sheet.cells[6].numeric_format == '0[.]0'
def test_from_dataframe():
df = pd.DataFrame({
'A': 1.,
'B': pd.Timestamp('20130102'),
'C': pd.Series(1, index=list(range(4)), dtype='float32'),
'D': np.array([False, True, False, False], dtype='bool'),
'S': pd.Categorical(["test", "train", "test", "train"]),
'T': 'foo'
})
sheet = ipysheet.from_dataframe(df)
assert len(sheet.cells) == 6
assert sheet.column_headers == ['A', 'B', 'C', 'D', 'S', 'T']
assert sheet.cells[0].value == [1., 1., 1., 1.]
assert sheet.cells[0].type == 'numeric'
assert sheet.cells[1].value == [
'2013/01/02', '2013/01/02', '2013/01/02', '2013/01/02'
]
assert sheet.cells[1].type == 'date'
assert sheet.cells[2].value == [1., 1., 1., 1.]
assert sheet.cells[2].type == 'numeric'
assert sheet.cells[3].value == [False, True, False, False]
assert sheet.cells[3].type == 'checkbox'
assert sheet.cells[4].value == ['test', 'train', 'test', 'train']
assert sheet.cells[4].type == 'text'
assert sheet.cells[5].value == ['foo', 'foo', 'foo', 'foo']
assert sheet.cells[5].type == 'text'
def on_upload_problemdir(self, change):
files = change['new']
file_names = list(files.keys())
if len(file_names) == 0:
return
probdir_name, _ = file_names[0].split('.')
print(probdir_name)
with tempfile.TemporaryDirectory() as tmpdirname:
print('created temporary directory', tmpdirname)
problemDirectory = os.path.join(tmpdirname, probdir_name)
os.mkdir(os.path.join(tmpdirname, probdir_name))
for fname in files.keys():
if "yml" in fname:
fp = open(os.path.join(problemDirectory, fname), 'wb')
fp.write(files[fname]["content"])
fp.close()
elif "pkl" in fname:
fp = open(os.path.join(problemDirectory, fname), 'wb')
fp.write(files[fname]["content"])
fp.close()
print(problemDirectory)
self.nmrproblem = nmrProblem.NMRproblem(problemDirectory)
if not isinstance(self.nmrproblem, type(None)):
self.prDirW.value = self.nmrproblem.problemDirectoryPath
# update other widgets based on contents of nmrproblem
self.updateSpectraWidgetsFromNMRproblem()
self.updateMoleculeWidgetsFromNMRproblem()
# create a view of the dataframe in nmrproblem
self.sheet1 = ipysheet.from_dataframe(self.nmrproblem.df)
self.dfWarningTextW.value = "Table Messages: None"
self.dfLayout.children = [
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
]
# create 1D 1H & C13 plots widget
self.H1C131DplotsLayout.children = [
self.createH1C13interactivePlot(), self.saveProblemButtonW
]
def test_from_to_dataframe():
df = pd.DataFrame({
'A': 1.,
'B': pd.Timestamp('20130102'),
'C': pd.Series(1, index=list(range(4)), dtype='float32'),
'D': np.array([False, True, False, False], dtype='bool'),
'S': pd.Categorical(["test", "train", "test", "train"]),
'T': 'foo'
})
df.loc[[0, 2], ['B']] = np.nan
sheet = ipysheet.from_dataframe(df)
df2 = ipysheet.to_dataframe(sheet)
a = np.array(df.values)
b = np.array(df2.values)
assert ((a == b) | (pd.isna(a) & pd.isna(b))).all()
def onButtonClicked(self, bttn):
self.debugLabel.value = bttn.description
# print("bttn", bttn, type(bttn), bttn.description)
if "Start New" in bttn.description:
self.debugLabel.value = self.problemNameW.value
# remove spaces from name
probdirname = self.problemNameW.value.replace(" ", "")
tmpdir = tempfile.TemporaryDirectory()
os.mkdir(os.path.join(tmpdir.name, probdirname))
self.nmrproblem = nmrProblem.NMRproblem(
os.path.join(tmpdir.name, probdirname))
# create a temporary problem directory
elif "Directory" in bttn.description:
self.nmrproblem = nmrProblem.NMRproblem.from_guidata()
if not isinstance(self.nmrproblem, type(None)):
self.prDirW.value = self.nmrproblem.problemDirectoryPath
# update other widgets based on contents of nmrproblem
self.updateSpectraWidgetsFromNMRproblem()
self.updateMoleculeWidgetsFromNMRproblem()
# create a view of the dataframe in nmrproblem
self.sheet1 = ipysheet.from_dataframe(self.nmrproblem.df)
self.dfWarningTextW.value = "Table Messages: None"
# dfLayout.children = [dfWarningTextW, qgrid1, dfButtonsLayout]
# create 1D 1H & C13 plots widget
self.H1C131DplotsLayout.children = [
self.createH1C13interactivePlot()
]
elif "update table" in bttn.description:
print("update table")
self.toggleDF.value = 'All'
ok = self.nmrproblem.updateDFtable(
ipysheet.to_dataframe(self.sheet1))
if ok:
self.nmrproblem.convertHSQCHMBCCOSYtoLists()
self.nmrproblem.update_attachedprotons_c13hyb()
self.sheet1 = ipysheet.from_dataframe(self.nmrproblem.df)
self.dfWarningTextW.value = "Table Messages: None"
else:
self.dfWarningTextW.value = "Table Messages: problems in table, please check it"
self.dfLayout.children = [
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
]
elif "update and run" in bttn.description:
self.toggleDF.value = 'All'
ok = self.nmrproblem.updateDFtable(
ipysheet.to_dataframe(self.sheet1))
if ok:
self.sheet1 = ipysheet.from_dataframe(self.nmrproblem.df)
self.dfWarningTextW.value = "Table Messages: None"
self.nmrproblem.dfToNumbers()
self.nmrproblem.convertHSQCHMBCCOSYtoLists()
self.nmrproblem.convertJHzToLists()
self.nmrproblem.update_attachedprotons_c13hyb()
# H1df_orig, C13df_orig = nmrProblem.readinChemShiftTables()
# H1df_orig, C13df_orig = read_in_cs_tables()
self.nmrproblem.calcProbDistFunctions(H1df_orig, C13df_orig)
self.nmrproblem.identify1HC13peaks()
self.nmrproblem.udic[0]['df'] = self.nmrproblem.H1df
self.nmrproblem.udic[1]['df'] = self.nmrproblem.C13df
# self.nmrproblem.iprobs = iprobs
self.nmrproblem.createInfoDataframes()
self.nmrproblem.calculate1H13CSpectra1D()
udic = self.nmrproblem.udic
self.nmrproblem.save1DspecInfotoUdic()
self.nmrproblem.create1H13Clabels(num_poss=3)
self.dfLayout.children = [
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
]
# create 1D 1H & C13 plots widget
self.H1C131DplotsLayout.children = [
self.createH1C13interactivePlot(), self.saveProblemButtonW
]
else:
self.dfWarningTextW.value = "Table Messages: problems in table, please check it"
self.dfLayout.children = [
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
]
elif "Spectra" in bttn.description:
self.nmrproblem.createInfoDataframes()
self.nmrproblem.save1DspecInfotoUdic()
self.updateSpectralInformationWidgetChanged()
self.nmrproblem.calculate1H13CSpectra1D()
self.H1C131DplotsLayout.children = [
self.createH1C13interactivePlot(), self.saveProblemButtonW
]
elif "Molecule" in bttn.description:
print("Molecule")
self.nmrproblem.update_molecule(self.moleculeAtomsW.value,
self.pGrpsW.value,
self.cGrpsW.value)
# create a view of the dataframe in nmrproblem
self.sheet1 = ipysheet.from_dataframe(self.nmrproblem.df)
self.dfWarningTextW.value = "Table Messages: None"
self.dfLayout.children = [
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
]
elif "Save Problem" in bttn.description:
yml_dict = self.nmrproblem.save_problem()
yml_str = yaml.dump(yml_dict, indent=4)
self.ymlText.value = yml_str
def __init__(self, nmrproblem=None):
super().__init__()
if not isinstance(nmrproblem, nmrProblem.NMRproblem):
self.nmrproblem = nmrproblem
self.df = pd.DataFrame()
else:
self.nmrproblem = nmrproblem
self.df = nmrproblem.df
# create debug label widget for output
self.debugLabel = widgets.Label(value="",
layout=widgets.Layout(width="400px"))
# create save problem widgets
self.saveProblemButtonW = widgets.Button(description="Save Problem")
# widgets to obtain problem working directory
self.prDirW = widgets.Text(value='',
placeholder='problem directory',
description='problem directory',
disabled=False)
self.prDirB = widgets.Button(description='Set Directory')
self.upload_problemdir = ipywidgets.widgets.FileUpload(
multiple=True,
description="Open Existing Problem ",
description_tooltip="choose all files in problem directory",
layout=widgets.Layout(width='300px'))
self.problemNameL = widgets.Label(value=" Problem Name",
layout=widgets.Layout(width='100px'))
self.spacerL = widgets.Label(value=" ",
layout=widgets.Layout(width='50px'))
self.problemNameW = widgets.Text(value="Problem Name",
description="",
layout=widgets.Layout(width='150px'))
self.newproblemB = widgets.Button(description="Start New Problem")
self.prDirLayout = widgets.HBox([
self.upload_problemdir, self.spacerL, self.problemNameL,
self.problemNameW, self.spacerL, self.newproblemB
])
# widgets to obtain info on the molecule
# number and tye of atoms in molecule
# number of proton resonances in molecule
# number of carbon resonance in molecule
self.moleculeAtomsW = widgets.Text(value='',
placeholder='atoms in molecule',
description='atoms',
disabled=False)
self.pGrpsW = widgets.IntText(value=1,
placeholder='H1 groups in spectrum',
description='H1 groups',
disabled=False)
self.cGrpsW = widgets.IntText(value=1,
description='C13 groups',
disabled=False)
self.moleculesSubmitB = widgets.Button(description="Update Molecule")
self.moleculeLayout = widgets.VBox([
self.moleculeAtomsW, self.pGrpsW, self.cGrpsW,
self.moleculesSubmitB
])
# widgets to set 1D spectral parameters for proton and carbon
self.pLabelW = widgets.Label("$^{1}H$")
self.pSpecWidthW = widgets.FloatText(value=12.0,
tooltip='proton spectral width',
description='sw (ppm)',
disabled=False)
self.pObsFreqW = widgets.FloatText(value=400.0,
description='obs (MHz)',
disabled=False)
self.pTofW = widgets.FloatText(value=5.0,
description='tof (ppm)',
diabled=False)
self.pSizeW = widgets.IntText(value=32768,
description='size (pts)',
disabled=False)
self.pLineBroadeningW = widgets.FloatText(value=0.5,
description='lb (Hz)',
disabled=False)
self.cLabelW = widgets.Label("$^{13}C$")
self.cSpecWidthW = widgets.FloatText(value=210.0,
description='sw (ppm)',
disabled=False)
self.cObsFreqW = widgets.FloatText(value=100.0,
description='obs (MHz)',
disabled=False)
self.cTofW = widgets.FloatText(value=5.0,
description='tof (ppm)',
diabled=False)
self.cSizeW = widgets.IntText(value=32768,
description='size (pts)',
disabled=False)
self.cLineBroadeningW = widgets.FloatText(value=0.5,
description='lb (Hz)',
disabled=False)
self.specSubmitB = widgets.Button(description="Update Spectra")
self.specLayout = widgets.HBox([
widgets.VBox([
self.pLabelW, self.pObsFreqW, self.pSpecWidthW, self.pTofW,
self.pSizeW, self.pLineBroadeningW, self.specSubmitB
]),
widgets.VBox([
self.cLabelW, self.cObsFreqW, self.cSpecWidthW, self.cTofW,
self.cSizeW, self.cLineBroadeningW
])
])
self.old = 'All'
self.new = 'ALL'
self.toggleDF = widgets.ToggleButtons(
options=['All', 'integrals-ppm', 'COSY', 'HSQC-HMBC'],
description='Display:',
disabled=False,
button_style='',
tooltips=[
'Show full Dataframe', 'Show COSY Input',
'Show HSQC/HMBC Input'
])
self.sheet1 = ipysheet.from_dataframe(self.df)
self.toggleDF.observe(self.toggleValue)
self.dfWarningTextW = widgets.Label("Table Messages: OK")
self.dfUpdateTableB = widgets.Button(description="update table")
self.dfRunAnalysisB = widgets.Button(description="update and run")
self.dfButtonsLayout = widgets.HBox(
[self.dfUpdateTableB, self.dfRunAnalysisB])
self.dfLayout = widgets.VBox([
self.toggleDF, self.dfWarningTextW, self.sheet1,
self.dfButtonsLayout
])
self.accordion = widgets.Accordion(children=[
self.prDirLayout, self.moleculeLayout, self.specLayout,
self.dfLayout
])
self.accordion.set_title(0, "Problem Directory")
self.accordion.set_title(1, "Molecule")
self.accordion.set_title(2, "Spectroscopy")
self.accordion.set_title(3, "DataSet")
self.page1 = widgets.VBox(
[self.accordion, self.saveProblemButtonW, self.debugLabel])
self.H1C131DplotsLayout = widgets.VBox(
[widgets.Output(), self.saveProblemButtonW])
self.ymlTitle = widgets.HTML("yml description of problem")
self.ymlText = widgets.Textarea(
layout=widgets.Layout(width="400px", height="500px"))
self.problemYML = widgets.VBox([self.ymlTitle, self.ymlText])
self.children = [self.page1, self.H1C131DplotsLayout, self.problemYML]
self.set_title(0, 'Problem Setup')
self.set_title(1, 'Problem Plots')
self.set_title(2, 'Problem YML')
self.upload_problemdir.observe(
lambda change: self.on_upload_problemdir(change), names='value')
self.moleculesSubmitB.on_click(self.onButtonClicked)
self.specSubmitB.on_click(self.onButtonClicked)
self.dfUpdateTableB.on_click(self.onButtonClicked)
self.dfRunAnalysisB.on_click(self.onButtonClicked)
self.saveProblemButtonW.on_click(self.onButtonClicked)
self.newproblemB.on_click(self.onButtonClicked)
def create_sheet(self, label_path: str):
""" creates ipysheet from file path to csv file
"""
df = pd.read_csv(label_path)
sheet = ipysheet.from_dataframe(df)
return sheet
# format_version: '1.4'
# jupytext_version: 1.2.1
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
import numpy as np
from RiverNetwork import RiverNetwork
from ipysheet import from_dataframe
import ipysheet
from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"
import pandas as pd
import networkx as nx
import matplotlib.pyplot as plt
# %load_ext autoreload
# %autoreload 2
df = pd.read_excel('data/network-structure-1.xlsx')
df
sheet = from_dataframe(df)
display(sheet)
ipysheet.pandas_loader.to_dataframe(sheet)