#!/usr/bin/env python
# encoding: utf-8
"""
A tool to display FT-ICR data-sets
to be embedded in jupyter notebook
MAD Sept 2019
This version requires ipympl (see: https://github.com/matplotlib/jupyter-matplotlib )
and the notebook to be opened with %matplotlib widget
"""
import os.path as op
import tables
import matplotlib.pyplot as plt
from ipywidgets import interact, fixed, HBox, VBox, GridBox, Label, Layout, Output, Button
import ipywidgets as widgets
from IPython.display import display, Markdown, HTML, Image
import numpy as np
from .. import FTICR
from ..NPKData import flatten, parsezoom
from .ipyfilechooser import FileChooser
from ..FTMS import FTMSData
from ..FTICR import FTICRData
# REACTIVE modify callback behaviour
# True is good for inline mode / False is better for notebook mode
REACTIVE = True
HEAVY = False
SIZEMAX = 8*1024*1024 # largest zone to display
NbMaxDisplayPeaks = 1000 # maximum number of peaks to display at once
# TOOLS FOR 2D FTICR
[docs]class MR(object):
"this class handles multiresolution datasets"
def __init__(self, name, report=True, Debug=False):
"name : filename of the msh5 multiresolution file"
self.SIZEMAX = SIZEMAX
self.name = name
self.data = [] # will contain all resolutions
self.absmax = 0.0 # will accumulates global absmax
self.load()
if self.absmax == 0.0:
self.compute_absmax()
self.axis1 = self.data[0].axis1
self.axis2 = self.data[0].axis2
# self.col0 = self.data[0].col
# self.row0 = self.data[0].row
self.highmass = self.data[0].highmass # a tuple (h1, h2)
self.Debug = Debug
if report: self.report()
[docs] def load(self):
"load from file"
self.data = []
for i in range(8):
try:
dl = FTICR.FTICRData(name=self.name, mode="onfile", group="resol%d"%(i+1))
except tables.NoSuchNodeError:
pass
else:
dl.unit='m/z'
self.data.append(dl)
[docs] def report(self):
"report object content"
print (self.name)
print(self.data[0])
print('=====================')
print('multiresolution data:\n#: Size')
for i,dl in enumerate(self.data):
print ("%d: %d x %d : %.0f Mpix"%( i+1, dl.size1, dl.size2, dl.size1*dl.size2/1024/1024 ))
def _report(self):
"low level report"
for i,dl in enumerate(self.data):
print(i+1)
print(dl)
[docs] def colmz(self,i):
"return a column with coordinate in m/z"
return self.col(self.axis2.mztoi(i))
[docs] def rowmz(self,i):
"return a row with coordinate in m/z"
return self.row(self.axis1.mztoi(i))
[docs] def col(self,i):
"return a column with coordinate in index"
return self.col(int(round(i)))
[docs] def row(self,i):
"return a row with coordinate in index"
return self.row(int(round(i)))
[docs] def to_display(self,zoom=((0,FTICR.FTMS.HighestMass),(0,FTICR.FTMS.HighestMass)), verbose=False):
"""
computes and return which dataset to display at a given zoom and scale level"
in: zoom = ((F1low, F1up), (F2low,F2up)) - in m/z
out: a tuple (data, zoomwindow), where data is a NPKData and zoomwindow an eventually recalibrated zoom window
so, if DATA is an MR() object and Zoom a defined window in m/z ((F1low, F1up), (F2low,F2up))
the sequence:
datasel, zz = DATA.to_display(Zoom)
datasel.display(zoom=zz, scale=...)
will display the selected zone with the best possible resolution
"""
z1,z2,z3,z4 = flatten(zoom)
# print ("m/z F1: %.1f - %.1f / F2 %.1f - %.1f"%(z1,z2,z3,z4))
z1,z2 = min(z1,z2), max(z1,z2)
z3,z4 = min(z3,z4), max(z3,z4)
for reso,dl in enumerate(self.data):
z11 = max(z1, dl.axis1.lowmass)
z33 = max(z3, dl.axis2.lowmass)
z22 = min(z2, dl.highmass[0])
z44 = min(z4, dl.highmass[1])
z1lo, z1up, z2lo, z2up = parsezoom(dl,(z11,z22,z33,z44))
sz = (z1lo-z1up)* (z2lo-z2up)
if sz < self.SIZEMAX:
#print (dl.size1,dl.size2, z1lo, z1up, z2lo, z2up, sz)
break
zooml = (dl.axis1.itomz(z1lo), dl.axis1.itomz(z1up), dl.axis2.itomz(z2lo), dl.axis2.itomz(z2up))
if verbose or self.Debug:
print ("zoom: F1 %.1f-%.1f / F2 %.1f-%.1f"%zooml)
print ("resolution level %d - %.1f Mpix zoom window"%(reso, sz/1024/1024))
return dl, zooml
[docs] def compute_absmax(self):
"computes largest point from smaller resolution, and propagates"
dsmall = self.data[-1]
self.absmax = dsmall.absmax
for dl in self.data:
dl._absmax = self.absmax
[docs]class MR_interact(MR):
def __init__(self, name, figsize=None, report=True, show=True, Debug=False):
"""
creates an interactive object.
if display is True (default) the graphical tool will be displayed.
"""
super(self.__class__, self).__init__(name, report=report, Debug=Debug)
self.vlayout = Layout(width='60px')
self.pltaxe = None
self.pltaxe1D = None
if figsize is None:
self.figsize = (10,8)
else:
self.figsize = (figsize[0]/2.54, figsize[1]/2.54, )
# self.reset_track()
self.check_fig()
if show: self.show()
[docs] def bb(self, name, desc, action, layout=None, tooltip=""):
"build a button into self"
if layout is None: layout = self.vlayout
butt = widgets.Button(description=desc, layout=layout, tooltip=tooltip)
butt.on_click(action)
setattr(self, name, butt)
##################### 2D #######################
[docs] def zoom_box(self):
"defines the zoom box widget"
# . F1 .
# F2 . F2
# . F1 .
self.scale = widgets.FloatLogSlider(description='scale:', value=1.0, min=-1, max=3, base=10, step=0.01,
layout=Layout(width='80%'), continuous_update=HEAVY)
wf = widgets.BoundedFloatText
ref = self.data[0]
style = {'description_width': 'initial'}
lay = Layout(width='100px', height='30px')
self.z1l = wf( min=ref.axis1.lowmass, max=ref.highmass[0],
tooltip='vertical zoom', style=style, layout=lay)
self.z1h = wf( min=ref.axis1.lowmass, max=ref.highmass[0],
style=style, layout=lay)
self.z2l = wf( min=ref.axis2.lowmass, max=ref.highmass[1],
style=style, layout=lay)
self.z2h = wf( min=ref.axis2.lowmass, max=ref.highmass[1],
style=style, layout=lay)
self.fullzoom()
self.bb('b_zupdate', 'Apply', lambda e : self.display(),
layout=Layout(width='100px'), tooltip="Set zoom to values")
self.bb('b_reset', 'Reset', self.reset,
layout=Layout(width='100px'), tooltip="Set zoom to values")
blank = widgets.HTML(" ",layout=lay)
label = widgets.HTML('Zoom Window (in <i>m/z</i>)')
innerbox = VBox([ label,
HBox([blank, self.z1h, blank]),
HBox([self.z2l, self.b_zupdate, self.z2h]),
HBox([blank, self.z1l, blank]),
]
)
action_box = VBox([blank ])
box = HBox([ self.b_reset, innerbox])
return innerbox
[docs] def spec_box(self):
"defines the spectral box widget"
self.scale = widgets.FloatSlider(description='scale:', value=1.0, min=1.0, max=20, step=0.1,
tooltip='Set display scale', layout=Layout(width='100px', height='400px'), continuous_update=HEAVY,
orientation='vertical')
self.scale.observe(self.ob)
self.bb('b_redraw', 'Redraw', lambda e : self.display(),
layout=Layout(width='100px'))
box = VBox([self.b_reset, self.scale, self.b_redraw])
return HBox([box, self.pltfig.canvas])
[docs] def scale_up(self, step):
self.scale.value *= 1.1892**step # 1.1892 is 4th root of 2.0
[docs] def show(self):
"actually show the graphical tool and the interactive spectrum"
display(self.box)
display(self.sbox)
self.display()
[docs] def ob(self, event):
"observe events and display"
if event['name'] != 'value':
return
self.display()
[docs] def display(self, zoom=None, scale=None):
"computes pictures (display in the SPIKE sense - not ipywidget one)"
if zoom is not None:
_zoom = zoom
else:
_zoom = (self.z1l.value, self.z1h.value, self.z2l.value, self.z2h.value)
if scale is not None:
self.scale.value = scale
datasel, zz = self.to_display(_zoom)
corner = (zz[1],zz[3])
reso = [corner[i]/datasel.axes(i+1).deltamz(corner[i]) for i in range(2)]
# print(corner, reso)
self.check_fig() # insure figure is there
# with self.out:
self.pltaxe.clear() # clear
datasel.display(zoom=zz, scale=self.scale.value, absmax=self.absmax,
xlabel='F2 m/z', ylabel='F1 m/z',
show=False, figure=self.pltaxe)
self.pltaxe.text(corner[1],corner[0],"D#%d R: %.0fx%.0f"%(self.data.index(datasel)+1, *reso))
[docs] def check_fig(self):
"create figure if missing"
if self.pltaxe is None:
plt.ioff()
# plt.clf()
fg,ax = plt.subplots(figsize=self.figsize)
self.pltaxe = ax
self.pltfig = fg
self.set_on_redraw()
self.box = self.zoom_box()
self.sbox = self.spec_box()
plt.ion()
[docs] def update(self, e):
"update internal zoom coordinates"
# self.track.append((self._zoom, self.scale))
# self.point = -1 # means last
#print('update')
xb = self.pltaxe.get_xbound()
yb = self.pltaxe.get_ybound()
#print( xb, yb)
self.z1l.value = yb[0]
self.z1h.value = yb[1]
self.z2l.value = xb[0]
self.z2h.value = xb[1]
[docs] def set_on_redraw(self):
def on_press(event):
print('you pressed', event.button, event.xdata, event.ydata)
def on_scroll(event):
self.scale_up(event.step)
cidd = self.pltfig.canvas.mpl_connect('draw_event', self.update)
cids = self.pltfig.canvas.mpl_connect('scroll_event', on_scroll)
# cidc = self.pltfig.canvas.mpl_connect('button_press_event', on_press)
[docs] def reset(self, b):
self.scale.value = 1.0
self.fullzoom()
self.reset_track()
self.display()
[docs] def fullzoom(self):
self.z1l.value = self.axis2.lowmass+0.01
self.z1h.value = self.highmass[0]
self.z2l.value = self.axis2.lowmass+0.01
self.z2h.value = self.highmass[1]
# ####### zoom track - experimental ########
[docs] def reset_track(self):
self.track = []
self.point = -1
# def back(self, *arg):
# self.point -= 1
# try:
# self._zoom, self.scale = self.track[self.point]
# except IndexError:
# self.point = -len(self.track)
# self._zoom, self.scale = self.track[0]
# self.update()
# self.display(redraw=True)
# def forw(self, *arg):
# self.point += 1
# try:
# self._zoom, self.scale = self.track[self.point]
# except IndexError:
# self._zoom, self.scale = self.track[-1]
# self.point = -1
# self.update()
# self.display(redraw=True)
# ##################### 1D ##################
[docs] def I1D(self):
"show the 1D selector"
self.r1D = None
self.t1D = ''
self.i1D = None
self.check_fig1D()
display(self.ext_box())
[docs] def check_fig1D(self):
if self.pltaxe1D is None:
fg,ax = plt.subplots(figsize=(1.5*self.figsize[0], 0.75*self.figsize[0]))
ax.text(0.1, 0.8, 'Empty - use "horiz" and "vert" buttons above')
self.pltaxe1D = ax
self.fig1D = fg
[docs] def ext_box(self):
"defines the interactive tools for 1D"
wf = widgets.BoundedFloatText
wi = widgets.BoundedIntText
ref = self.data[0]
style = {'description_width': 'initial'}
lay = Layout(width='120px', height='30px')
lay2 = Layout(width='50px', height='30px')
self.z1 = wf( value=300.0, min=ref.axis1.lowmass, max=ref.highmass[0], description='F1', style=style, layout=lay)
self.z2 = wf( value=300.0, min=ref.axis2.lowmass, max=ref.highmass[1], description='F2', style=style, layout=lay)
self.horiz = wi( value=1, min=1, max=20, style=style, layout=lay2)
self.vert = wi( value=1, min=1, max=20, style=style, description="/", layout=lay2)
def lrow(b, inc=0):
rint = int(round(ref.axis1.mztoi(self.z1.value)))
if inc !=0:
rint += inc
self.z1.value = ref.axis1.itomz(rint)
if self.t1D == 'col':
self.pltaxe1D.clear()
self.r1D = None
if self.b_accu.value == 'sum' and self.r1D is not None:
self.r1D += ref.row(rint)
else:
self.r1D = ref.row(rint)
self.t1D = 'row'
self.i1D = rint
self.display1D()
def lrowp1(b):
lrow(b,-1)
def lrowm1(b):
lrow(b,1)
def lcol(b, inc=0):
rint = int(round(ref.axis2.mztoi(self.z2.value)))
if inc !=0:
rint += inc
self.z2.value = ref.axis2.itomz(rint)
if self.t1D == 'row':
self.pltaxe1D.clear()
self.r1D = None
if self.b_accu.value == 'sum' and self.r1D is not None:
self.r1D += ref.col(rint)
else:
self.r1D = ref.col(rint)
self.t1D = 'col'
self.i1D = rint
self.display1D()
def lcolp1(b):
lcol(b,-1)
def lcolm1(b):
lcol(b,1)
def on_press(event):
v = self.r1D.axis1.mztoi(event.xdata)
if self.t1D == 'col':
self.z1.value = v
elif self.t1D == 'row':
self.z2.value = v
cids = self.fig1D.canvas.mpl_connect('button_press_event', on_press)
self.bb('b_row', 'horiz', lrow, layout=Layout(width='60px'), tooltip='extract an horizontal row')
self.bb('b_rowp1', '+1', lrowp1, layout=Layout(width='30px'), tooltip='next row up')
self.bb('b_rowm1', '-1', lrowm1, layout=Layout(width='30px'), tooltip='next row down')
self.bb('b_col', 'vert', lcol, layout=Layout(width='60px'), tooltip='extract a vertical col')
self.bb('b_colp1', '+1', lcolp1, layout=Layout(width='30px'), tooltip='next col right')
self.bb('b_colm1', '-1', lcolm1, layout=Layout(width='30px'), tooltip='next col left')
self.b_accu = widgets.Dropdown(options=['off', 'graphic', 'sum'],
value='off', description='Accumulate plots while scanning:', style=style)
return VBox([ widgets.HTML('<h3>Extract 1D MS Spectrum going through given F1-F2 coordinates</h3>'),
HBox([widgets.HTML("<B>coord:</B>"),self.z1,
self.b_row, self.b_rowp1, self.b_rowm1, self.b_accu]),
HBox([widgets.HTML("<B>coord:</B>"),self.z2,
self.b_col, self.b_colp1, self.b_colm1])])
[docs] def display1D(self):
"display the selected 1D"
if self.t1D == 'row':
title = 'horizontal extract at F1=%f m/z (index %d)'%(self.z1.value, self.i1D)
label = str(self.z1.value)
elif self.t1D == 'col':
title = 'vertical extract at F2=%f m/z (index %d)'%(self.z2.value, self.i1D)
label = str(self.z2.value)
if self.b_accu.value != 'graphic':
self.pltaxe1D.clear()
label = None
self.r1D.display(xlabel='m/z', show=False, figure=self.pltaxe1D, new_fig=False, label=label, title=title)
[docs]class MSPeaker(object):
"a peak-picker for MS experiments"
def __init__(self, npkd, pkname):
if not isinstance(npkd, FTMSData):
raise Exception('This modules requires a FTMS Dataset')
self.npkd = npkd
self.pkname = pkname
self.zoom = widgets.FloatRangeSlider(value=[npkd.axis1.lowmass, npkd.axis1.highmass],
min=npkd.axis1.lowmass, max=npkd.axis1.highmass, step=0.1,
layout=Layout(width='100%'), description='zoom',
continuous_update=False, readout=True, readout_format='.1f',)
self.zoom.observe(self.display)
self.tlabel = Label('threshold (x noise level):')
self.thresh = widgets.FloatLogSlider(value=20.0,
min=np.log10(1), max=2.0, base=10, step=0.01, layout=Layout(width='30%'),
continuous_update=False, readout=True, readout_format='.1f')
self.thresh.observe(self.pickpeak)
self.peak_mode = widgets.Dropdown(options=['marker', 'bar'],value='marker',description='show as')
self.peak_mode.observe(self.display)
self.bexport = widgets.Button(description="Export",layout=Layout(width='7%'),
button_style='success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Export to csv file')
self.bexport.on_click(self.pkexport)
self.bprint = widgets.Button(description="Print", layout=Layout(width='7%'),
button_style='success', tooltip='Print to screen')
self.bprint.on_click(self.pkprint)
self.bdone = widgets.Button(description="Done", layout=Layout(width='7%'),
button_style='warning', tooltip='Fix results')
self.bdone.on_click(self.done)
#self.spec = Output(layout={'border': '1px solid black'})
self.out = Output(layout={'border': '1px solid red'})
display( VBox([self.zoom,
HBox([self.tlabel, self.thresh, self.peak_mode, self.bprint, self.bexport, self.bdone])
]) )
self.fig, self.ax = plt.subplots()
self.npkd.set_unit('m/z').peakpick(autothresh=self.thresh.value, verbose=False, zoom=self.zoom.value).centroid()
self.display()
display(self.out)
[docs] def pkprint(self,event):
self.out.clear_output(wait=True)
with self.out:
display(HTML(self.npkd.pk2pandas().to_html()))
#print(self.pklist())
[docs] def pkexport(self,event):
"exports the peaklist to file"
with open(self.pkname,'w') as FPK:
print(self.pklist(),file=FPK)
print('Peak list stored in ',self.pkname)
[docs] def pklist(self):
"creates peaklist"
text = ["m/z\t\tInt.(%)\tR\tarea(a.u.)"]
data = self.npkd
intmax = max(data.peaks.intens)/100
for pk in data.peaks:
mz = data.axis1.itomz(pk.pos)
Dm = 0.5*(data.axis1.itomz(pk.pos-pk.width) - data.axis1.itomz(pk.pos+pk.width))
area = pk.intens*Dm
l = "%.6f\t%.1f\t%.0f\t%.0f"%(mz, pk.intens/intmax, round(mz/Dm,-3), area)
text.append(l)
return "\n".join(text)
[docs] def display(self, event={'name':'value'}):
"display spectrum and peaks"
if event['name']=='value': # event is passed by GUI - make it optionnal
self.ax.clear()
self.npkd.display(new_fig=False, figure=self.ax, zoom=self.zoom.value)
try:
self.npkd.display_peaks(peak_label=True, peak_mode=self.peak_mode.value, figure=self.ax, zoom=self.zoom.value, NbMaxPeaks=NbMaxDisplayPeaks)
x = self.zoom.value
y = [self.npkd.peaks.threshold]*2
self.ax.plot(x,y,':r')
self.ax.annotate('%d peaks detected'%len(self.npkd.peaks) ,(0.05,0.95), xycoords='figure fraction')
except:
pass
[docs] def pickpeak(self, event):
"interactive wrapper to peakpick"
if event['name']=='value':
self.pp()
[docs] def pp(self):
"do the peak-picking calling pp().centroid()"
#self.spec.clear_output(wait=True)
self.npkd.set_unit('m/z').peakpick(autothresh=self.thresh.value, verbose=False, zoom=self.zoom.value).centroid()
self.display()
[docs] def done(self, event):
"exit GUI"
for w in [self.zoom, self.thresh, self.peak_mode, self.bprint, self.bexport, self.bdone]:
w.close()
self.tlabel.value = "threshold %.2f noise level"%self.thresh.value
# self.display()
[docs]class Calib(object):
"a simple tool to show and modify calibration cste"
def __init__(self, data):
self.data = data
self.res = [data.axis1.calibA, data.axis1.calibB, data.axis1.calibC]
self.A = widgets.FloatText(value=data.axis1.calibA, description="A")
self.B = widgets.FloatText(value=data.axis1.calibB, description="B")
self.C = widgets.FloatText(value=data.axis1.calibC, description="C")
self.bupdate = widgets.Button(description="Update",
button_style='success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='set current data-sets to displayed values')
self.bupdate.on_click(self.update)
self.bback = widgets.Button(description="Restore",
button_style='success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='restore dataset to initial values')
self.bback.on_click(self.back)
display(VBox([ HBox([self.A, widgets.Label('Hz/Th')]),
HBox([self.B, widgets.Label('Hz')]),
HBox([self.C, widgets.Label('Hz/Th^2')]),
HBox([self.bupdate, self.bback])]))
[docs] def update(self,event):
self.data.axis1.calibA = self.A.value
self.data.axis1.calibB = self.B.value
self.data.axis1.calibC = self.C.value
print("Set - don't forget to rerun the Peak Picker")
[docs] def back(self,event):
self.data.axis1.calibA = self.res[0]
self.data.axis1.calibB = self.res[1]
self.data.axis1.calibC = self.res[2]
self.A.value = self.res[0]
self.B.value = self.res[1]
self.C.value = self.res[2]
Colors = ('black','red','blue','green','orange',
'blueviolet','crimson','turquoise','indigo',
'magenta','gold','pink','purple','salmon','darkblue','sienna')
[docs]class SpforSuper(object):
"a holder for SuperImpose"
def __init__(self, i, name):
j = i%len(Colors)
self.name = widgets.Text(value=name, layout=Layout(width='70%'))
self.color = widgets.Dropdown(options=Colors,value=Colors[j],layout=Layout(width='10%'))
self.direct = widgets.Dropdown(options=['up','down','off'],value='off', layout=Layout(width='10%'))
self.me = HBox([widgets.HTML(value="<b>%d</b>"%i),self.name, self.color,self.direct])
self.fig = False
[docs] def display(self):
if self.name != 'None' and self.direct.value != 'off':
scale = 1
if self.direct.value == 'up':
mult = 1
elif self.direct.value == 'down':
mult = -1
else:
return
FTICRData(name=self.name.value).set_unit('m/z').mult(mult).display(
new_fig=self.fig,
scale=scale,
color=self.color.value,
label=op.basename(op.dirname(self.name.value)))
[docs]class SuperImpose(object):
"a tool to superimpose spectra"
def __init__(self, base=None, filetype='*.msh5', N=None):
if N is None:
N = int(input('how many spectra do you want to compare: '))
self.Chooser = FileChooser(base=base, filetype=filetype, mode='r', show=False)
self.bsel = widgets.Button(description='Copy',layout=Layout(width='10%'),
button_style='info', # 'success', 'info', 'warning', 'danger' or ''
tooltip='copy selected data-set to entry below')
self.to = widgets.IntText(value=1,min=1,max=N,layout=Layout(width='10%'))
self.bsel.on_click(self.copy)
self.bdisplay = widgets.Button(description='Display',layout=Layout(width='10%'),
button_style='info', # 'success', 'info', 'warning', 'danger' or ''
tooltip='display superimposition')
self.bdisplay.on_click(self.display)
self.spec = Output(layout={'border': '1px solid black'})
self.DataList = [SpforSuper(i+1,'None') for i in range(N)]
self.DataList[0].color.value = 'black'
self.DataList[0].fig = True # switches on the very first one
[docs] def Show(self):
display(widgets.Label('Select a file, and click on the Copy button to copy it to the chosen slot'))
self.Chooser.show()
display(HBox([self.bsel, widgets.Label('to'), self.to]))
display(VBox([sp.me for sp in self.DataList]))
display(self.bdisplay)
display(self.spec)
[docs] def copy(self, event):
if self.to.value <1 or self.to.value >len(self.DataList):
print('Destination is out of range !')
else:
self.DataList[self.to.value-1].name.value = self.Chooser.file
self.DataList[self.to.value-1].direct.value = 'up'
self.to.value = min(self.to.value, len(self.DataList)) +1
[docs] def display(self, event):
self.spec.clear_output(wait=True)
for i,s in enumerate(self.DataList):
with self.spec:
s.display()
[docs]class MS2Dscene(HBox):
"a widget to set all MS tools into one screen"
def __init__(self, show=True, root='/'):
super(self.__class__, self).__init__()
# DATA
self.MR2D = None # The MR2D object
# GUI tools
self.FC = FileChooser(root, filetype='*.msh5', mode='r')
self.bdisp2D = Button(description='Load 2D',layout=Layout(width='20%'),
button_style='success', tooltip='load and display interactive 2D map')
self.bdisp2D.on_click(self.load2D)
# GUI
self.header = Output()
with self.header:
display(Markdown('---\n# Select a file, and choose a tool'))
display(self.FC)
display(self.bdisp2D)
self.out2D = Output() # the area where 2D is shown
with self.out2D:
display(HTML("<br><br><h3><i><center>No Data</center></i></h3>"))
# self.outpp2D = Output() # the area where peak picking is shown
# with self.outpp2D:
# display(HTML("<br><br><h3><i><center>No Data</center></i></h3>"))
self.out1D = Output() # the area where 1D is shown
with self.out1D:
display(HTML("<br><br><h3><i><center>No Data</center></i></h3>"))
self.outinfo = Output() # the area where info is shown
with self.outinfo:
display(HTML("<br><br><h3><i><center>No Data</center></i></h3>"))
# GUI set-up and show
self.tabs = widgets.Tab()
self.tabs.children = [ self.out2D, self.out1D, self.outinfo ]
self.tabs.set_title(0, '2D Display')
self.tabs.set_title(1, '1D extraction')
# self.tabs.set_title(2, 'Peak Picking')
self.tabs.set_title(2, 'info')
# self.tabs = VBox([ self.out2D, self.outpp2D, self.out1D, self.outinfo ])
self.box = VBox([ self.header,
self.tabs
])
# self.box = VBox([self.title,
# self.FC,
# HBox([self.bdisp2D, self.bpp2D, self.bdisp1D])
# ])
if show:
display(self.box)
[docs] def load2D(self, e):
"create 2D object and display"
self.out2D.clear_output(wait=True)
# self.outpp2D.clear_output(wait=True)
self.out1D.clear_output(wait=True)
self.outinfo.clear_output(wait=True)
try:
self.MR2D = MR_interact(self.FC.selected,
report=False, show=False, figsize=(15,15), Debug=False)
except FileNotFoundError:
self.MR2D = None
with self.out2D:
display(HTML("<br><br><h3><i><center>No Data or wrong Data</center></i></h3>"))
if self.MR2D is not None:
with self.out2D:
self.MR2D.show()
# display(self.MR2D.box)
# display(self.MR2D.sbox)
with self.out1D:
self.MR2D.I1D()
# with self.outpp2D:
# display(self.MR2D.box) # copie of the main pane
# display(self.MR2D.sbox)
with self.outinfo:
self.MR2D.report()
print()