[Bokeh]Getting `TypeError: Object of type Polygon is not JSON serializable`










0















First time posting in stackoverflow. Hope you guys are doing well.
Recently, I am trying to create a filterable Bokeh graph to graph a US map base on the filter an user select. However, when I try to fit a geometry to ColumnDataSource. It is giving me an error: TypeError: Object of type Polygon is not JSON serializable when I run show(figure)



The code below shows how I want to update geometry to ColumnDataSource and I get an error



# <------- This is where the graph starts------->

# reset the graph
reset_output()

# import data
data = gpd.read_file("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", encoding="utf-8")
data1 = data[~data.STUSPS.isin(['AK','AS', 'GU', 'HI', 'PR','MP', 'VI'])]
data2 = data[data.STUSPS.isin(['TX', 'UT'])]

# get a list of unique value
unique_state = sorted(list(data2.NAME.unique()))
select = Select(title="State", options=unique_state)

# get data into ColumnDataSource
source=ColumnDataSource(ColumnDataSource.from_df(data2.loc[:]))

# crate filtered dataframe
filteredSource = ColumnDataSource(data=dict(STUSPS=,NAME=,ALAND=))

columns = [TableColumn(field="NAME",title="NAME",sortable=True),
TableColumn(field="STUSPS",title="STUSPS",sortable=True),
TableColumn(field="ALAND",title="ALAND",sortable=True),
TableColumn(field="geometry",title="geometry",sortable=True)]

data_table=DataTable(source=filteredSource,columns=columns, width=800 )

# <---- Call back starts ---->
callback = CustomJS(args=dict(source=source,
filteredSource=filteredSource,
data_table=data_table), code="""
var data = source.data;
var f = cb_obj.value;
var d2 = filteredSource.data;
d2['STUSPS']=
d2['NAME']=
d2['ALAND']=
d2['geometry']=


for(i = 0; i < data['NAME'].length;i++)

if(data['NAME'][i]==f)

d2['STUSPS'].push(data['STUSPS'][i])
d2['NAME'].push(data['NAME'][i])
d2['ALAND'].push(data['ALAND'][i])
d2['geometry'].push(data['geometry'][i])




filteredSource.change.emit()
// trigger change on datatable
data_table.change.emit()

""")

select.js_on_change('value',callback)

layout = column(widgetbox(select, data_table))

# output_file("filter.html", title="filter example")

show(layout)


Afterwards, I saw an example directly fitting shape file to dictionary or dataframe which may solve the problem. Here is the link:
Bokeh Mapping Counties
However, when I using the code to graph it. it is giving me



ValueError: Out of range float values are not JSON compliant


This is the code I run:



import shapefile
import itertools

shp = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", "rb")
dbf = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.dbf", "rb")
sf = shapefile.Reader(shp=shp, dbf=dbf)

lats =
lons =
ct_name =
st_id =
ct_state_name =
for shprec in sf.shapeRecords():
st_id.append(int(shprec.record[0]))
ct_name.append(shprec.record[5])
ct_state_name.append(shprec.record[4])
lat, lon = map(list, zip(*shprec.shape.points))
indices = shprec.shape.parts.tolist()
lat = [lat[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lon = [lon[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lat = list(itertools.chain.from_iterable(lat))
lon = list(itertools.chain.from_iterable(lon))
lats.append(lat)
lons.append(lon)

map_data = pd.DataFrame('x': lats, 'y': lons, 'state': st_id, 'county_name': ct_name, 'ct_state_name': ct_state_name)
map_data_m = map_data[map_data.ct_state_name.isin(['NJ'])]

source = ColumnDataSource(map_data_m)

TOOLS="pan,wheel_zoom,box_zoom,reset,hover,save"

p = figure(title="Title", tools=TOOLS,
x_axis_location=None, y_axis_location=None)
p.grid.grid_line_color = None

p.patches('x', 'y', source=source,
fill_color='color', fill_alpha=0.7,
line_color="white", line_width=0.5)

show(p)


anyone who is able to help me to resolve either of the question? I have been stuck for few days. Thanks a lot!










share|improve this question






















  • Are there any NaN or inf values in your dataset? Reference: stackoverflow.com/questions/38821132/…

    – user2908623
    Nov 14 '18 at 21:29











  • hello @user2908623. thank you os much for replying back. I checked and there is no NaN in both my x and y...>_<

    – David Pu
    Nov 14 '18 at 22:01
















0















First time posting in stackoverflow. Hope you guys are doing well.
Recently, I am trying to create a filterable Bokeh graph to graph a US map base on the filter an user select. However, when I try to fit a geometry to ColumnDataSource. It is giving me an error: TypeError: Object of type Polygon is not JSON serializable when I run show(figure)



The code below shows how I want to update geometry to ColumnDataSource and I get an error



# <------- This is where the graph starts------->

# reset the graph
reset_output()

# import data
data = gpd.read_file("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", encoding="utf-8")
data1 = data[~data.STUSPS.isin(['AK','AS', 'GU', 'HI', 'PR','MP', 'VI'])]
data2 = data[data.STUSPS.isin(['TX', 'UT'])]

# get a list of unique value
unique_state = sorted(list(data2.NAME.unique()))
select = Select(title="State", options=unique_state)

# get data into ColumnDataSource
source=ColumnDataSource(ColumnDataSource.from_df(data2.loc[:]))

# crate filtered dataframe
filteredSource = ColumnDataSource(data=dict(STUSPS=,NAME=,ALAND=))

columns = [TableColumn(field="NAME",title="NAME",sortable=True),
TableColumn(field="STUSPS",title="STUSPS",sortable=True),
TableColumn(field="ALAND",title="ALAND",sortable=True),
TableColumn(field="geometry",title="geometry",sortable=True)]

data_table=DataTable(source=filteredSource,columns=columns, width=800 )

# <---- Call back starts ---->
callback = CustomJS(args=dict(source=source,
filteredSource=filteredSource,
data_table=data_table), code="""
var data = source.data;
var f = cb_obj.value;
var d2 = filteredSource.data;
d2['STUSPS']=
d2['NAME']=
d2['ALAND']=
d2['geometry']=


for(i = 0; i < data['NAME'].length;i++)

if(data['NAME'][i]==f)

d2['STUSPS'].push(data['STUSPS'][i])
d2['NAME'].push(data['NAME'][i])
d2['ALAND'].push(data['ALAND'][i])
d2['geometry'].push(data['geometry'][i])




filteredSource.change.emit()
// trigger change on datatable
data_table.change.emit()

""")

select.js_on_change('value',callback)

layout = column(widgetbox(select, data_table))

# output_file("filter.html", title="filter example")

show(layout)


Afterwards, I saw an example directly fitting shape file to dictionary or dataframe which may solve the problem. Here is the link:
Bokeh Mapping Counties
However, when I using the code to graph it. it is giving me



ValueError: Out of range float values are not JSON compliant


This is the code I run:



import shapefile
import itertools

shp = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", "rb")
dbf = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.dbf", "rb")
sf = shapefile.Reader(shp=shp, dbf=dbf)

lats =
lons =
ct_name =
st_id =
ct_state_name =
for shprec in sf.shapeRecords():
st_id.append(int(shprec.record[0]))
ct_name.append(shprec.record[5])
ct_state_name.append(shprec.record[4])
lat, lon = map(list, zip(*shprec.shape.points))
indices = shprec.shape.parts.tolist()
lat = [lat[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lon = [lon[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lat = list(itertools.chain.from_iterable(lat))
lon = list(itertools.chain.from_iterable(lon))
lats.append(lat)
lons.append(lon)

map_data = pd.DataFrame('x': lats, 'y': lons, 'state': st_id, 'county_name': ct_name, 'ct_state_name': ct_state_name)
map_data_m = map_data[map_data.ct_state_name.isin(['NJ'])]

source = ColumnDataSource(map_data_m)

TOOLS="pan,wheel_zoom,box_zoom,reset,hover,save"

p = figure(title="Title", tools=TOOLS,
x_axis_location=None, y_axis_location=None)
p.grid.grid_line_color = None

p.patches('x', 'y', source=source,
fill_color='color', fill_alpha=0.7,
line_color="white", line_width=0.5)

show(p)


anyone who is able to help me to resolve either of the question? I have been stuck for few days. Thanks a lot!










share|improve this question






















  • Are there any NaN or inf values in your dataset? Reference: stackoverflow.com/questions/38821132/…

    – user2908623
    Nov 14 '18 at 21:29











  • hello @user2908623. thank you os much for replying back. I checked and there is no NaN in both my x and y...>_<

    – David Pu
    Nov 14 '18 at 22:01














0












0








0








First time posting in stackoverflow. Hope you guys are doing well.
Recently, I am trying to create a filterable Bokeh graph to graph a US map base on the filter an user select. However, when I try to fit a geometry to ColumnDataSource. It is giving me an error: TypeError: Object of type Polygon is not JSON serializable when I run show(figure)



The code below shows how I want to update geometry to ColumnDataSource and I get an error



# <------- This is where the graph starts------->

# reset the graph
reset_output()

# import data
data = gpd.read_file("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", encoding="utf-8")
data1 = data[~data.STUSPS.isin(['AK','AS', 'GU', 'HI', 'PR','MP', 'VI'])]
data2 = data[data.STUSPS.isin(['TX', 'UT'])]

# get a list of unique value
unique_state = sorted(list(data2.NAME.unique()))
select = Select(title="State", options=unique_state)

# get data into ColumnDataSource
source=ColumnDataSource(ColumnDataSource.from_df(data2.loc[:]))

# crate filtered dataframe
filteredSource = ColumnDataSource(data=dict(STUSPS=,NAME=,ALAND=))

columns = [TableColumn(field="NAME",title="NAME",sortable=True),
TableColumn(field="STUSPS",title="STUSPS",sortable=True),
TableColumn(field="ALAND",title="ALAND",sortable=True),
TableColumn(field="geometry",title="geometry",sortable=True)]

data_table=DataTable(source=filteredSource,columns=columns, width=800 )

# <---- Call back starts ---->
callback = CustomJS(args=dict(source=source,
filteredSource=filteredSource,
data_table=data_table), code="""
var data = source.data;
var f = cb_obj.value;
var d2 = filteredSource.data;
d2['STUSPS']=
d2['NAME']=
d2['ALAND']=
d2['geometry']=


for(i = 0; i < data['NAME'].length;i++)

if(data['NAME'][i]==f)

d2['STUSPS'].push(data['STUSPS'][i])
d2['NAME'].push(data['NAME'][i])
d2['ALAND'].push(data['ALAND'][i])
d2['geometry'].push(data['geometry'][i])




filteredSource.change.emit()
// trigger change on datatable
data_table.change.emit()

""")

select.js_on_change('value',callback)

layout = column(widgetbox(select, data_table))

# output_file("filter.html", title="filter example")

show(layout)


Afterwards, I saw an example directly fitting shape file to dictionary or dataframe which may solve the problem. Here is the link:
Bokeh Mapping Counties
However, when I using the code to graph it. it is giving me



ValueError: Out of range float values are not JSON compliant


This is the code I run:



import shapefile
import itertools

shp = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", "rb")
dbf = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.dbf", "rb")
sf = shapefile.Reader(shp=shp, dbf=dbf)

lats =
lons =
ct_name =
st_id =
ct_state_name =
for shprec in sf.shapeRecords():
st_id.append(int(shprec.record[0]))
ct_name.append(shprec.record[5])
ct_state_name.append(shprec.record[4])
lat, lon = map(list, zip(*shprec.shape.points))
indices = shprec.shape.parts.tolist()
lat = [lat[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lon = [lon[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lat = list(itertools.chain.from_iterable(lat))
lon = list(itertools.chain.from_iterable(lon))
lats.append(lat)
lons.append(lon)

map_data = pd.DataFrame('x': lats, 'y': lons, 'state': st_id, 'county_name': ct_name, 'ct_state_name': ct_state_name)
map_data_m = map_data[map_data.ct_state_name.isin(['NJ'])]

source = ColumnDataSource(map_data_m)

TOOLS="pan,wheel_zoom,box_zoom,reset,hover,save"

p = figure(title="Title", tools=TOOLS,
x_axis_location=None, y_axis_location=None)
p.grid.grid_line_color = None

p.patches('x', 'y', source=source,
fill_color='color', fill_alpha=0.7,
line_color="white", line_width=0.5)

show(p)


anyone who is able to help me to resolve either of the question? I have been stuck for few days. Thanks a lot!










share|improve this question














First time posting in stackoverflow. Hope you guys are doing well.
Recently, I am trying to create a filterable Bokeh graph to graph a US map base on the filter an user select. However, when I try to fit a geometry to ColumnDataSource. It is giving me an error: TypeError: Object of type Polygon is not JSON serializable when I run show(figure)



The code below shows how I want to update geometry to ColumnDataSource and I get an error



# <------- This is where the graph starts------->

# reset the graph
reset_output()

# import data
data = gpd.read_file("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", encoding="utf-8")
data1 = data[~data.STUSPS.isin(['AK','AS', 'GU', 'HI', 'PR','MP', 'VI'])]
data2 = data[data.STUSPS.isin(['TX', 'UT'])]

# get a list of unique value
unique_state = sorted(list(data2.NAME.unique()))
select = Select(title="State", options=unique_state)

# get data into ColumnDataSource
source=ColumnDataSource(ColumnDataSource.from_df(data2.loc[:]))

# crate filtered dataframe
filteredSource = ColumnDataSource(data=dict(STUSPS=,NAME=,ALAND=))

columns = [TableColumn(field="NAME",title="NAME",sortable=True),
TableColumn(field="STUSPS",title="STUSPS",sortable=True),
TableColumn(field="ALAND",title="ALAND",sortable=True),
TableColumn(field="geometry",title="geometry",sortable=True)]

data_table=DataTable(source=filteredSource,columns=columns, width=800 )

# <---- Call back starts ---->
callback = CustomJS(args=dict(source=source,
filteredSource=filteredSource,
data_table=data_table), code="""
var data = source.data;
var f = cb_obj.value;
var d2 = filteredSource.data;
d2['STUSPS']=
d2['NAME']=
d2['ALAND']=
d2['geometry']=


for(i = 0; i < data['NAME'].length;i++)

if(data['NAME'][i]==f)

d2['STUSPS'].push(data['STUSPS'][i])
d2['NAME'].push(data['NAME'][i])
d2['ALAND'].push(data['ALAND'][i])
d2['geometry'].push(data['geometry'][i])




filteredSource.change.emit()
// trigger change on datatable
data_table.change.emit()

""")

select.js_on_change('value',callback)

layout = column(widgetbox(select, data_table))

# output_file("filter.html", title="filter example")

show(layout)


Afterwards, I saw an example directly fitting shape file to dictionary or dataframe which may solve the problem. Here is the link:
Bokeh Mapping Counties
However, when I using the code to graph it. it is giving me



ValueError: Out of range float values are not JSON compliant


This is the code I run:



import shapefile
import itertools

shp = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.shp", "rb")
dbf = open("/Users/xxxx/Desktop/cb_2015_us_state_500k/cb_2015_us_state_500k.dbf", "rb")
sf = shapefile.Reader(shp=shp, dbf=dbf)

lats =
lons =
ct_name =
st_id =
ct_state_name =
for shprec in sf.shapeRecords():
st_id.append(int(shprec.record[0]))
ct_name.append(shprec.record[5])
ct_state_name.append(shprec.record[4])
lat, lon = map(list, zip(*shprec.shape.points))
indices = shprec.shape.parts.tolist()
lat = [lat[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lon = [lon[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lat = list(itertools.chain.from_iterable(lat))
lon = list(itertools.chain.from_iterable(lon))
lats.append(lat)
lons.append(lon)

map_data = pd.DataFrame('x': lats, 'y': lons, 'state': st_id, 'county_name': ct_name, 'ct_state_name': ct_state_name)
map_data_m = map_data[map_data.ct_state_name.isin(['NJ'])]

source = ColumnDataSource(map_data_m)

TOOLS="pan,wheel_zoom,box_zoom,reset,hover,save"

p = figure(title="Title", tools=TOOLS,
x_axis_location=None, y_axis_location=None)
p.grid.grid_line_color = None

p.patches('x', 'y', source=source,
fill_color='color', fill_alpha=0.7,
line_color="white", line_width=0.5)

show(p)


anyone who is able to help me to resolve either of the question? I have been stuck for few days. Thanks a lot!







python-3.x bokeh






share|improve this question













share|improve this question











share|improve this question




share|improve this question










asked Nov 14 '18 at 21:10









David PuDavid Pu

11




11












  • Are there any NaN or inf values in your dataset? Reference: stackoverflow.com/questions/38821132/…

    – user2908623
    Nov 14 '18 at 21:29











  • hello @user2908623. thank you os much for replying back. I checked and there is no NaN in both my x and y...>_<

    – David Pu
    Nov 14 '18 at 22:01


















  • Are there any NaN or inf values in your dataset? Reference: stackoverflow.com/questions/38821132/…

    – user2908623
    Nov 14 '18 at 21:29











  • hello @user2908623. thank you os much for replying back. I checked and there is no NaN in both my x and y...>_<

    – David Pu
    Nov 14 '18 at 22:01

















Are there any NaN or inf values in your dataset? Reference: stackoverflow.com/questions/38821132/…

– user2908623
Nov 14 '18 at 21:29





Are there any NaN or inf values in your dataset? Reference: stackoverflow.com/questions/38821132/…

– user2908623
Nov 14 '18 at 21:29













hello @user2908623. thank you os much for replying back. I checked and there is no NaN in both my x and y...>_<

– David Pu
Nov 14 '18 at 22:01






hello @user2908623. thank you os much for replying back. I checked and there is no NaN in both my x and y...>_<

– David Pu
Nov 14 '18 at 22:01













1 Answer
1






active

oldest

votes


















0














Could you check if there are no infinite numbers in the dataset?
Reference: https://stackoverflow.com/a/47085304/2908623






share|improve this answer























  • Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

    – David Pu
    Nov 19 '18 at 19:19










Your Answer






StackExchange.ifUsing("editor", function ()
StackExchange.using("externalEditor", function ()
StackExchange.using("snippets", function ()
StackExchange.snippets.init();
);
);
, "code-snippets");

StackExchange.ready(function()
var channelOptions =
tags: "".split(" "),
id: "1"
;
initTagRenderer("".split(" "), "".split(" "), channelOptions);

StackExchange.using("externalEditor", function()
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled)
StackExchange.using("snippets", function()
createEditor();
);

else
createEditor();

);

function createEditor()
StackExchange.prepareEditor(
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader:
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
,
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
);



);













draft saved

draft discarded


















StackExchange.ready(
function ()
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53308766%2fbokehgetting-typeerror-object-of-type-polygon-is-not-json-serializable%23new-answer', 'question_page');

);

Post as a guest















Required, but never shown

























1 Answer
1






active

oldest

votes








1 Answer
1






active

oldest

votes









active

oldest

votes






active

oldest

votes









0














Could you check if there are no infinite numbers in the dataset?
Reference: https://stackoverflow.com/a/47085304/2908623






share|improve this answer























  • Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

    – David Pu
    Nov 19 '18 at 19:19















0














Could you check if there are no infinite numbers in the dataset?
Reference: https://stackoverflow.com/a/47085304/2908623






share|improve this answer























  • Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

    – David Pu
    Nov 19 '18 at 19:19













0












0








0







Could you check if there are no infinite numbers in the dataset?
Reference: https://stackoverflow.com/a/47085304/2908623






share|improve this answer













Could you check if there are no infinite numbers in the dataset?
Reference: https://stackoverflow.com/a/47085304/2908623







share|improve this answer












share|improve this answer



share|improve this answer










answered Nov 14 '18 at 22:31









user2908623user2908623

476




476












  • Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

    – David Pu
    Nov 19 '18 at 19:19

















  • Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

    – David Pu
    Nov 19 '18 at 19:19
















Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

– David Pu
Nov 19 '18 at 19:19





Hello @user2908623 thanks for replying back again. I have seen that reference and tried all the solutions. Somehow after I upgraded my Bokeh to the newest version. it is working now. Really thank you for your help! :D

– David Pu
Nov 19 '18 at 19:19



















draft saved

draft discarded
















































Thanks for contributing an answer to Stack Overflow!


  • Please be sure to answer the question. Provide details and share your research!

But avoid


  • Asking for help, clarification, or responding to other answers.

  • Making statements based on opinion; back them up with references or personal experience.

To learn more, see our tips on writing great answers.




draft saved


draft discarded














StackExchange.ready(
function ()
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53308766%2fbokehgetting-typeerror-object-of-type-polygon-is-not-json-serializable%23new-answer', 'question_page');

);

Post as a guest















Required, but never shown





















































Required, but never shown














Required, but never shown












Required, but never shown







Required, but never shown

































Required, but never shown














Required, but never shown












Required, but never shown







Required, but never shown







這個網誌中的熱門文章

How to read a connectionString WITH PROVIDER in .NET Core?

In R, how to develop a multiplot heatmap.2 figure showing key labels successfully

Museum of Modern and Contemporary Art of Trento and Rovereto