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ARIA Challenge
Write some JavaScript in aria.js to give increment and decrement functionality.
Use ARIA live regions so that screen readers announce when the count changes.
0
Increment
Decrement


3. Getting Started¶
This chapter highlights several features of GeoMesa, along with tutorials that describe for getting started with these capabilities.
3.1. GeoMesa Accumulo¶
The GeoMesa Accumulo Quick Start tutorial is the fastest and easiest way to get started with GeoMesa. It is a good stepping-stone on the path to the other tutorials that present increasingly involved examples of how to use GeoMesa. It shows how to write custom Java code to ingest and query data in Accumulo with GeoMesa, and visualize the changes being made in GeoServer.
3.2. GeoDocker: Bootstrapping GeoMesa Accumulo and Spark on AWS¶
Getting started with spatio-temporal analysis with GeoMesa, Accumulo, and Spark on Amazon Web Services (AWS) is incredibly simple, thanks to the Geodocker project. The guide below describes how to bootstrap a GeoMesa Accumulo cluster using Amazon ElasticMapReduce (EMR) and Docker in order to ingest and query sample GDELT data.
See /tutorials/geodocker-geomesa-spark-on-aws.
3.3. GeoMesa Kafka¶
The GeoMesa Kakfa Quick Start tutorial shows how to write custom Java code to produce and consume messages in Apache Kafka using GeoMesa, query the data and replay the messages in a Kafka topic to achieve an earlier state, and visualize the changes being made in Kafka with GeoServer.
3.4. Storm Analysis¶
GeoMesa can leverage the Apache Storm distributed computation system to ingest and analyze geospatial data in near real time. The GeoMesa Storm Quick Start tutorial shows how to use Kafka, GeoMesa, and Storm to parse Open Street Map data files and ingest them into Accumulo.
3.5. GeoJSON¶
GeoMesa provides built-in integration with GeoJSON. GeoMesa provides a GeoJSON API that allows for the indexing and querying of GeoJSON data without using the GeoTools API–all data and operations are pure JSON. The API also includes a REST endpoint for web integration.
See GeoMesa GeoJSON.


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Have a software project that needs to get done?
Let us help you!
We are passionate about our craft. Software development requires intricate attention to details. Every i's need to be dotted, every t's need to be crossed, and every code line need to end with semicolon. Software projects need to delivered in time and on point, let us help you with that.
We develop customized web-based systems for your enterprise needs, tailored to you unique processes and workflow.
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A good website not only need to be beautifule, but most importantly clear and informative. Content Management Systems can help you with this.
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A web system that allows customer to submit complaints that will be processed by support personnel, leading up to claims approval and payment.
A front-end for an OPC/SCADA that shows graphical status of some electrical distribution (DB) boxes spread across the nation. The application interacts with an OPC server to acquire the status, gather reports, and show alerts. and also able to initiate actions such as resetting a circuit breaker switch.
Sales and billing system for a courier business to manage it's contract customers and their billings. This includes the registration process for contract customers, products and pricing, rebates and discounts, disputes management, and invoice generation.
A front-end for an OPC/SCADA setup that shows graphical status of communication devices of a military agency. The application interacts with an OPC server to acquire the status, gather reports, and alerts.
Starting with a feedback form from the corporate website, a suggestion, complaint, or enquiry is then routed to appropriate departments for action. A designated customer service representative then replies with a proper follow-up.
A system to compose and collect questions for exams. Question will go through various QA to ensure its quality. Exam papers can then be generated on the fly based on pre-define templates.
A system to register and assign KPI items and areas for employee. Outcomes can then be rated and assessed. Integrated with SAP Human Resource module.
A system to register reports of misuse and tampering of company assets which SITREP and further investigations can be done. SLA is put is place to ensure responsiveness.
Management and approval of budget allocation, requests and returns from division to departments and projects. Integrated with SAP Investment Management module.
A system to manage leasing request, commisioning, terminations, and billing of fibre optic infrastructure and services. Intergrates with third party Asset Management System and SAP Billing module.
Provides methods for submission of ideas which then can be peer-evaluated, endorsed, and implemented. Outcome then can tracked and monitored using reports and scorecards.
An executive dashboard and statistics for projects management. Integrated with Microsoft Enterprise Project Management Server.
Provides means for suppliers and contractors to submit their application to be vendors for an organization. Modules include registration, evaluation, performance tracking, training, event and surveys.
Allows manufacturer to acquire certification for their products from a government agency. Includes assessement, surveillance, quotation generation, and QR code distribution modules.
* Some projects are kept discreet in their description as requested by our partners and clients.
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{% extends "bootstrap.html" %} {% block title %}Setup IFSensor{% endblock %} {% block navigation %} IFSensor project {% endblock %} {% block content %}
The installation was a success. Everything is ready to go!
When you are ready, then let's go to the dashboard


com.hazelcast.cluster
Interfaces
ClusterService
Joiner
JoinOperation
MulticastListener
Classes
AbstractJoiner
AuthenticationFailureOperation
AuthorizationOperation
BindOperation
ClusterDataSerializerHook
ClusterProxy
ClusterServiceImpl
ConfigCheck
ConfigMismatchOperation
FinalizeJoinOperation
GroupMismatchOperation
HeartbeatOperation
JoinCheckOperation
JoinMessage
JoinRequest
JoinRequestOperation
MasterClaimOperation
MasterConfirmationOperation
MasterDiscoveryOperation
MemberAttributeChangedOperation
MemberInfo
MemberInfoUpdateOperation
MemberRemoveOperation
MergeClustersOperation
MulticastJoiner
MulticastService
NodeMulticastListener
PostJoinOperation
PrepareMergeOperation
SetMasterOperation
TcpIpJoiner
TcpIpJoinerOverAWS
Enums
MemberAttributeOperationType
Exceptions
ConfigMismatchException


Your one and only provider of delicious pizzas
Enjoy your favorite choice!!
This one is enough for one individual
This one is good for 3 or 4 people
This one is good for 6 or 7 people
Pizza Size ksh =
Pizza Crust ksh =
Pizza Toppings ksh =
Delivery Fee ksh =


§235-37 Apportionment; sales factor; nontangible personalty. Sales, other than sales of tangible personal property, are in this State if:
(1) The income-producing activity is performed in this State; or
(2) The income-producing activity is performed both in and outside this State and a greater proportion of the income-producing activity is performed in this State than in any other state, based on costs of performance. [L 1967, c 33, pt of §1; HRS §235-37]


IN THE HIGH COURT OF PUNJAB AND HARYANA AT CHANDIGARH CWP No.15070 of 2016 (O&M) 1 IN THE HIGH COURT OF PUNJAB AND HARYANA AT CHANDIGARH CWP No.15070 of 2016 (O&M) DATE OF DECISION:03.04.2018 M/s Luxmi Screening Plant ... Petitioner Versus State of Punjab and others ... Respondents CORAM: HON'BLE MR. JUSTICE AJAY KUMAR MITTAL HON'BLE MR. JUSTICE ANUPINDER SINGH GREWAL Present: Dr. Surya Parkash, Advocate for the petitioner. Ms. Reeta Kohli, Senior Advocate with Mr. Rahul Sharma, Advocate for respondents No.2 and 3. Mr. Jagmohan S. Ghuman, Deputy Advocate General, Punjab. **** ANUPINDER SINGH GREWAL, J.
1. The petitioner has impugned the notice dated 24.07.2014 (Annexure P-6) issued under Section 31-A of the Air (Prevention and Control of Pollution) Act, 1981 and notice dated 24.07.2014 (Annexure P-7) issued under Section 33-A of the Water (Prevention and Control of Pollution) Act, 1974 vide which the petitioner has been directed to close down the operation of the industry and remove the entire plant and machinery. It has further challenged the order dated 04.03.2015 (Annexure P-9) whereby it has been directed to comply with the directions issued by the Board and the order dated 19.05.2016 (Annexure P-11) whereby the appeal of the petitioner has been dismissed by the Appellate 1 of 4 ::: Downloaded on - 06-05-2018 00:23:33 ::: IN THE HIGH COURT OF PUNJAB AND HARYANA AT CHANDIGARH CWP No.15070 of 2016 (O&M) 2 Authority.
2. The petitioner is stated to be in the business of Screening- Cum-Washing of gravel and has set up the industry at killa Nos.35//23/2(4-16), 24(3-11), total measuring 8K-7M (Brani) land, in the year 2008. It is stated that the unit of the petitioner after complying with all the norms and conditions has been functioning since the year 2008 and the respondents have arbitrarily and illegally directed it to be shut down.
3. Learned counsel for the petitioner has contended that the unit of the petitioner is complying with the provisions of the Water (Prevention and Control of Pollution) Act, 1974 (hereinafter referred as 'Water Act') and Air (Prevention and Control of Pollution) Act, 1981 (hereinafter referred as 'Air Act'). He has drawn the attention of this Court to the report of the Superintending Engineer and Executive Engineer, Department of Drainage dated 14.12.2015 wherein the distance of the petitioner unit from the river bank was found to be over 300 feet and hence it was permissible for the petitioner to run the unit.
4. Learned counsel for the respondents has contended that as the unit of the petitioner fell within the embankment of river Ghaggar, it has rightly been directed to be closed.
5. We have heard learned counsel for the parties.
6. A perusal of the order passed by the Appellate Authority shows that the unit of the petitioner fell within the embankment of river Ghaggar. The unit of the petitioner was inspected by a Committee comprising Officers of various departments i.e. Sub Divisional Magistrate, General Manager, DIC-cum-mining officer Ajitgarh (Mohali), Environmental Engineer, Punjab Pollution Control Board, Ajitgarh (Mohali), Environmental 2 of 4 ::: Downloaded on - 06-05-2018 00:23:34 ::: IN THE HIGH COURT OF PUNJAB AND HARYANA AT CHANDIGARH CWP No.15070 of 2016 (O&M) 3 Engineer, Punjab Pollution Control Board, Ajitgarh (Mohali), Executive Engineer, Drainage Division, Department of Irrigation, Ajitgarh (Mohali), Divisional Forest Officer, Ajitgarh (Mohali) and District Town Planner, Ajitgarh (Mohali) and it was found to be falling in the river bed. The Committee is stated to have been constituted by the Deputy Commissioner, SAS Nagar, Mohali in terms of the order passed on 13.08.2013 in CWP No.21899 of 2012 titled as Surmukh Singh Vs. State of Punjab and others. This Committee had visited stone-crusher/screening-cum-washing plants located within jurisdiction of SAS Nagar, District Mohali. In the report, the unit of the appellant was shown at Serial No.84. It, therefore, fell in the Flood Protection Embankment and was in violation of the Act.
7. The Appellate Authority has disregarded the report of the Superintending Engineer and Executive Engineer, Department of Drainage Patiala dated 14.12.2015 on the ground that although in the report it is stated that there is no guide bank on the outer side of the plant of the appellant, but the site plan enclosed with the report of the drainage department clearly depicts a guide bank on the side of the site of the industry, thereby showing the site of the industry where the water will be guided by the guide bank. It is also mentioned that the specific purpose of the Flood Protection Embankment is to restrict the flood water and the unit of the appellant as per the report of the Site Appraisal Committee is situated within the Flood Protection Embankment of river Ghaggar. This report is also signed by the Executive Engineer of Drainage Department.
8. It is, thus, patent that as per the report of the Committee the unit of the petitioner falls within the embankment of river Ghaggar. Therefore, we do not find any manifest illegality in the impugned orders 3 of 4 ::: Downloaded on - 06-05-2018 00:23:34 ::: IN THE HIGH COURT OF PUNJAB AND HARYANA AT CHANDIGARH CWP No.15070 of 2016 (O&M) 4 which would warrant interference in writ jurisdiction. Consequently, the petition stands dismissed.
(AJAY KUMAR MITTAL) (ANUPINDER SINGH GREWAL)
JUDGE JUDGE
April 03, 2018
jt
Whether speaking/reasoned : Yes / No
Whether reportable : Yes / No
4 of 4
::: Downloaded on - 06-05-2018 00:23:34 :::


Note: To complete the procedures in this document, you must be assigned a role having the necessary permissions. To determine your role, follow the directions in Participant roles. To view a list of permissions associated with a given role, see Permissions, roles, and tools. For a basic understanding of roles and permissions, see Permissions and Roles: Overview.
The Gradebook automatically calculates a course grade that's a percentage of current points scored out of the total points possible for all assignments. Therefore, the autocalculated course grade can be accurate only when all assignments are graded. If ungraded assignments are present, they will count as 0 points scored, and the resulting course grade will not accurately reflect the student's cumulative score.
By default, the option for displaying a course grade is disabled,
and students see only their scores for each of their assignments. To
display a course grade to students, click Grade Options
,
place a checkmark in the box next to Display cumulative score,
course grades and calculated assignment grades to students now
,
and then click Save
.
To override the autocalculated course grade, and enter a grade to display that reflects a student's true running course grade, follow these steps:
Gradebook
. If you are
not already on the Overview page of the Gradebook tool, click
Overview
near the top of the window.
Course Grade
.
Note: When manually entering a course grade, you must
use the appropriate grade type for the Gradebook in which you are
working. For example, if the course is graded on a simple letter grade
scale, you will only be able to enter the letters
A
, B
,
C
, D
, or
F
. If the course is graded on a standard
letter grade scale, you will also be able to add
+
(plus sign) or -
(minus sign) to the letter grade. If the course is graded on a
pass/fail scale, you will only be able to enter the letters
S
or F
.
Save
.
If you have overridden a course grade, and you want to revert back to the autocalculated grade, do the following:
Gradebook
. If you are not already
on the Overview page of the Gradebook tool, click Overview
near the top of the window.
Course Grade
.
Save
.
Note: You will have to delete the manually entered
grade and click Save
for each grade you want to change back.


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This is a good place to leave a boat to travel overland, especially to Peru. If you are heading to the Galapagos from Panama, coming here first instead of going on the rhum line only adds 130 NM to the passage. There are excellent boatyard and repair facilities here.
Position 2°13.01' S, 80°55.28' W. (marina)
See Ecuador Clearance for full details of clearance procedure.
All international vessels coming to Ecuador, by law, must have an Agent. The following agent represents cruisers at the present time: Julia Yturralde NOE SHIPPING (juliayde@hotmail.es). We recommend you request a quote in advance.
As you approach the port call the Port Captain on Ch 16. There is very little likelihood that you will get a response, but it is protocol to call.
As soon as the yacht is in radio range, the captain must report directly to Puerto Lucia Yacht Club on VHF Ch16 (08:00 to 18:00hrs) and follow instructions. Normally the yacht will be asked to anchor a short safe distance from the marina lighthouse on the starboard side past the entrance. If arriving outside working hours, the yacht must anchor outside the entrance buoy and clear in the following morning.
Agents charge each tourist boat approx. US$250, plus additional fees for immigration and customs etc., amounting to an average total cost of between US$300 - $400 for clearance. Be sure to get a written quotation beforehand and ask the agent to write down every charge and itemize what it is for. Get an official Factura (receipt) for everything.
The Yacht Club and the agency will arrange for the Authorities to come on board the yacht, having helped with the preparation of the necessary documents.
The various fees to be paid, usually on departure, are collected by the Port Captain.
Last updated July 2016.
Approach
The peninsula here runs NW to SE and is built up all along its length.
The SE corner is called la Libertad and is a fishing village with many fishing boats anchored off. Do not be tempted to anchor here!
The NW end is called Salinas and, essentially, is a resort town and home to the exclusive Salinas Yacht Club. Bursting at its seams with 2,500 members, visitors are not able to berth here. However in August 2014 mooring buoys were installed off the yacht club that can be rented.
Puerto Lucia
In the middle is Puerto Lucia, a private development of condos, gym, swimming pool, hotel, restaurant and marina with boatyard run by Stewart Yachts & Services. The marina welcomes visitors and whilst everyone can normallly be accommodated, it is wise to book in advance. Puerto Lucia is easily identified by six apartment blocks, the one in the middle having a distinctive white roof in the shape of a pyramid.
Anchor at the entrance to the marina and call them on 19 Alpha. If you do not have Alpha channels you will need to call them on your mobile phone - 278 3180. One of the Marineros will come to fetch you in a dory. Do not be tempted to go alongside the fuel dock as it is frequently used by fishing boats to load supplies, fuel and bulk ice. Beware that remaining at anchoring in the entrance will incur the same charge as berthing in the marina.
The marina is not large and has floating pontoons with water and electricity on both its northern and southern sides. The north pontoons all have short fingers, the south pontoons are much cheaper for berthing but have three short fingers only. Mooring is Med-style. There is surge in this marina (less on the cheaper south side) and so most boats put out long shore lines.
Security in the marina is excellent as there are guards on 24 hour duty, and there is strict control at the main gates that lead into the club and marina. All visitors must pre-resister at the marina office.
Noonsite has received a number of negative reports about this marina in the past which can be found adjacent under 'reports' and below under 'comments'. Topics include high costs, unreliable electricity & Wifi and crude oil pollution in the harbour.
Salinas
There is excellent provisioning here and most services (including a large chandlery) can be found just a short taxi ride from the marina.
See comment below about on-going developments in Salinas.
Last updated July 2016.


Nelson Rolihlahla Mandela
Brief origin
Rolihlahla Mandela was born into the Madiba clan in the village of Mvezo, in the Eastern Cape, on 18 July 1918. His mother was Nonqaphi Nosekeni and his father was Nkosi Mphakanyiswa Gadla Mandela, principal counsellor to the Acting King of the Thembu people, Jongintaba Dalindyebo. In 1930, when he was 12 years old, his father died and the young Rolihlahla became a ward of Jongintaba at the Great Place in Mqhekezweni1.Some major life events
- July 18, 1918 — Born to Hendry Mphakanyiswa, a Thembu chief, and Nosekeni Qunu in the Umtata district of the Transkei, at a time when virtually all of Africa was under European colonial rule.
- 1940 — Expelled from University of Fort Hare, a leading institution for blacks, for role in a student strike.
- 1942 — Joins African National Congress, South Africa’s main campaigner for black equality.
- June 4, 1948 — National Party, dominated by white Dutch-descended Afrikaners, is elected to power and begins installing apartheid, a system of complete racial segregation. It will rule without interruption for 46 years.
- 1952 — Mandela leads the Defiance Campaign, encouraging people to break racial separation laws. Convicted under Suppression of Communism Act, banned from attending gatherings and leaving Johannesburg. Passes exam to qualify as an attorney and, with Tambo, forms the first black law partnership in the country.
- 1958 — Marries social worker Winnie Nomzamo Madikizela after divorcing Evelyn Mase, his first wife.
- 1961 — Helps establish ANC guerrilla wing, Umkhonto we Sizwe, or Spear of the Nation.
- April 20, 1964 — Charged with sabotage, Mandela delivered a statement during his trial in Pretoria that revealed the depth of his resolve in the fight against apartheid and his willingness to lay down his life in an effort to end white racist rule.
“During my lifetime I have dedicated myself to this struggle of the African people, I have fought against white domination, and I have fought against black domination. I have
cherished the ideal of a democratic and free society in which all persons live together in harmony
and with equal opportunities. It is an ideal which I hope to live for and to achieve. But if needs
be, it is an ideal for which I am prepared to die.”
--- Nelson Mandela
Two months later, he and seven other defendants were sentenced to life in prison.


Match Play. 0-0 to 11. How should Red play 62?
pips Red=160 White=110
(CorrectAnswer= 0/0, ErrorScore= 0)
Not an easy problem. Over the board 24/18, 13/11 was played but that allows White to hit with tempo from one of stripped outer board points.
That play ties for second place with 13/5 and 24/18, 5/3.
With a racing deficit Red does better to keep the goalkeeper and await developments. He should build his board and see what happens. The correct move is 13/7, 5/3. The three plays tied for second place are all errors, but only just.
That play ties for second place with 13/5 and 24/18, 5/3.
With a racing deficit Red does better to keep the goalkeeper and await developments. He should build his board and see what happens. The correct move is 13/7, 5/3. The three plays tied for second place are all errors, but only just.
1. Cubeful 2-ply 13/7 5/3 Eq.: -0.456 0.298 0.047 0.002 - 0.702 0.193 0.011 2. Cubeful 2-ply 13/7 8/6 Eq.: -0.486 (-0.031) 0.285 0.047 0.002 - 0.715 0.191 0.011 3. Cubeful 2-ply 24/18 13/11 Eq.: -0.491 (-0.035) 0.289 0.042 0.001 - 0.711 0.201 0.009 4. Cubeful 2-ply 13/5 Eq.: -0.508 (-0.053) 0.277 0.043 0.001 - 0.723 0.191 0.009 5. Cubeful 2-ply 24/16 Eq.: -0.511 (-0.056) 0.279 0.040 0.001 - 0.721 0.196 0.008


- The aim of the game is to fill in the board with the missing digits while satisfying the constraints.
- There is only one unique solution which does this.
Constraints
- Numbers cannot be repeated within a row or column.
- The icons between the squares are additional inequality constraints.


[gecode-users] Compiling statically
Guido Tack
tack at ps.uni-sb.de
Sat Nov 7 19:00:40 CET 2009
The Gecode libs themselves cannot be linked statically (e.g. against
libstdc++), they're just archives of object files, after all. One
problem with the current build system is that if you've built dynamic
libs before and they're still in the directory, they will be used for
linking. If you --enable-static --disable-dynamic in a fresh source
directory, the executables should be linked against the static Gecode
libs.
Another question is whether they should be linked fully statically
after configuring with --enable-static, or just use the static Gecode
libs but still link libstdc++ dynamically. No idea what's more useful
there - but I guess we could add -static to the linker options.
Cheers,
Guido
Lars Kotthoff wrote:
>> we currently don't support creating both static and dynamic
>> libraries,
>> and our configure script has a bug, it doesn't switch off dynamic
>> libs
>> when you say --enable-static. Please try --enable-static --disable-
>> dynamic, I think it should work.
>
> Thanks Guido, unfortunately it still doesn't work. The produced
> libraries and
> binaries are still dynamically linked and the Makefile doesn't
> contain "-static"
> anywhere.
>
> Lars
>
> _______________________________________________
> Gecode users mailing list
> users at gecode.org
> https://www.gecode.org/mailman/listinfo/gecode-users
More information about the gecode-users
mailing list


---
layout: archive
title: Lean Prover Zulip Chat Archive
permalink: 113489newmembers/95093Operatorsections.html
---
The archive URL format has changed. Please find this page at:
https://leanprover-community.github.io/archive/stream/113489-new-members/topic/Operator.20sections.html


Delivery and failure
Our delivery states are:
- Sending
- Delivered
- Phone number or email address does not exist
- Inbox not accepting messages right now
- Phone not accepting messages right now
- Technical failure
Sending
All messages start in the ‘Sending’ state.
This means that we have accepted the message. It’s waiting in a queue to be sent to our email or text message delivery partners.
Delivered
This means the message is in the person’s email inbox or on their phone.
We can’t tell you if they’ve read it – to do so would require invasive and unreliable tracking techniques.
Phone number or email address does not exist
You’re still billed for text messages to non-existant phone numbers.
You need to remove these email addresses or phone numbers from your database.
Inbox not accepting messages right now
This can happen for a number of reasons, eg the user’s inbox was full.
You can choose to retry these messages later or not.
Phone not accepting messages right now
This means the user’s phone was full or hasn’t been switched on in the last 72 hours.
You’re still billed for these messages.
You can choose to retry these messages later or not.
Technical failure
This means there is a problem with the connection between Notify and our email or text message delivery partners.
Messages still being retried are marked as ’Sending’. We mark messages as ‘Technical failure’ once we’ve given up.
You won’t be billed for these messages.
You need to retry these messages yourself later.


Steps to reproduce
- Open Firebug and select the HTML panel
- Inspect the blue
<div>
above
- Select the Style side panel
- Click on the value
green
of the CSS property color
to open the inline editor
-
Press
R
⇒ RED
should be offered as value
-
Press
Up
⇒ ROYALBLUE
should be offered as value
-
Press
Down
⇒ RED
should be offered as value
- Press
Home
-
Press
Up
⇒ purple
(in lowercase) should be offered as value
-
Press
Down
⇒ red
(in lowercase) should be offered as value
Expected Result
-
There should always be suggestions when pressing
Up
/Down
-
The suggestions should always represent the next value in alphabetical order


--- layout: post title: Access properties of object properties in a WebDrawer template categories: [] tags: webdrawer serviceapi status: publish type: post published: true meta: {} ---
Some things in the Razor templates of the ServiceAPI and WebDrawer are not all that obvious, one is how to display the name of the record author. In an earlier post I created a custom search form, this video shows a custom search results template and how to display the name (or any other property) of the record author.
In a future release accessing properties of property objects should become a little more straightforward.


Cleaning a Parcellated Dictionary¶
Using the tools in parc_ts_dictionary, a dictionary is generated containing all of the items that would be conventionally used in denoising the fMRI time signal. This dictionary can then be used to generated denoised data with the denoise function within denoise_ts_dict. The denoise function is seen as follows:
denoise(parc_dict,
hpf_before_regression,
scrub_criteria_dictionary,
interpolation_method,
noise_comps_dict,
clean_comps_dict,
high_pass,
low_pass)
parc_dict: this is a dictionary generated by parc_ts_dictionary that has been loaded into memory.
hpf_before_regression: This argument specifies whether or not the nuisance regressors and the time-signals of interest (i.e. the parcellated time-signals) before the nuisance regressors are regressed from the parcellated time-signals. If you do not want to do this, set to False. Otherwise set to the desired high-pass cutoff point.
scrub_criteria_dictionary: This argument allows the user to define how scrubbing should be conducted. If you do not want to do scrubbing, set this argument to False. If you want to do scrubbing, there are a few different configuration options for the dictionary
{‘std_dvars’ : 1.2, ‘framewise_displacement’ : 0.5}
{‘Uniform’ : [0.8, [‘std_dvars’, ‘framewise_displacement’]]}
In the first example, any timepoints with std_dvars > 1.2, and framewise_displacement > 0.5 will be scrubbed. Any number of variables found under the confounds dictionary can be used to do scrubbing, with any cutoff point. In the second example, Uniform scrubbing is specified, with 0.8 meaning that the best 80% of timepoints should be kept. The sub-list with std_dvars and framewise_displacement says that std_dvars and framewise_displacement should be used to determine what the best volumes are. This means the two metrics will be demeaned and variance normalized and then added together, and the 80% of volumes with the lowest score on the combined metric will be kept. Any variables under the confounds dictionary (that are not groupings such as motion_regs_24) can be used to construct these dictionaries.
INSERT MORE DETAILS ABOUT THIS z-transform, confounds, etc.
interpolation_method: Can choose between ‘linear’, ‘cubic_spline’, and ‘spectral’. The spectral denoising takes the longest but is expected to perform the best (this is based off of the technique presented in Power’s 2014 NeuroImage paper/Anish Mitra’s work)
noise_comps_dict: this dictionary configures what nuisance signals will be removed from the parcellated timeseries. Each element represents an entry to the confounds dictionary, where the key is the name of the confound (or group of confounds) to be regressed, and the entry is either False or an integer, which specifies whether the nuisance regressors should be reduced by PCA and if so how many principal components should be kept. Some examples are seen below:
#Include 24 motion parameters as regressors
denoise_dict = {'motion_regs_twentyfour' : False}
#Include 24 motion parameters as regressors, reduced through PCA to 10 regressors
denoise_dict = {'motion_regs_twentyfour' : 10}
#Include WM/CSF/GSR + motion parameters as regressors
denoise_dict = {'wmcsfgsr' : False, 'motion_regs_twentyfour' : False}
#Include WM/CSF/GSR + ICA-AROMA Noise Timeseries as regressors
denoise_dict = {'wmcsfgsr' : False, 'aroma_noise_ics' : False}
#Skip nuisance regression
denoise_dict = False
clean_comps_dict: The formatting of this dictionary is identical to the noise_comps_dict, but this dictionary is used for specifying components whose variance you do not want to be removed from the parcellated timeseries. During the denoising process a linear model will be fit to the parcellated time-series using both the signals specified by the noise_comps_dict and clean_comps_dict, but only the signal explained by the noise_comps_dict will be removed.
high_pass: The cutoff frequency for the high-pass filter to be used in denoising. If you want to skip the high-pass filter, set to False.
low_pass: The cutoff frequency for the low-pass filter to be used in denoising. If you want tot skip the low-pass filter, set to False.
Running the function will output a dictionary containing the cleaned parcellated signal along with the settings used for denoising, other QC variables, and variables copied from the input dictionary. This includes:
cleaned_timeseries: The cleaned signal after denoising with shape <n_regions, n_timepoints>. Any scrubbed timepoints, or timepoints removed at beginning of the scan will be NaN
denoising_settings.json: The settings specified when using the denoise function
dvars_pre_cleaning: DVARS calculated pre-cleaning on all input parcels (timepoints skipped at the beginning of the run + the next timepoint after the initial skipped timepoints will have DVARS set to -0.001)
dvars_post_cleaning: DVARS calculated post-cleaning on all input parcels (scrubbed timepoints, timepoints at beginning of the run, and timepoints following scrubbed timepoints will have DVARS set to -0.001)
- dvars_stats.json: Different statistics about DVARS including (removed TPs not included in any stats):
mean_dvars_pre_cleaning: temporal average dvars before cleaning
mean_dvars_post_cleaning: temporal average dvars after cleaning
dvars_remaining_ratio: mean_dvars_post_cleaning/mean_dvars_pre_cleaning
max_dvars_pre_cleaning: highest dvars value before cleaning
max_dvars_post_cleaning: highest dvars value after cleaning
file_path_dictionary.json: copied from input, containing file paths involved in constructing the parcellated dictionary
general_info.json: copied from input, containing relevant info such as the name of the subject/session, parcel labels, number of high motion and fd timepoints (calculated from fMRIPREP), etc.
good_timepoint_inds: the indices for timepoints with defined signal (i.e. everything but the volumes dropped at the beginning of the scan and scrubbed timepoints)
labels: another copy of the parcel label names
mean_roi_signal_intensities.json: the mean signal intensities for raw fMRIPREP calculated csf, global_signal, and white_matter variables
median_ts_intensities: The spatial mean of the temporal median of all voxels/vertices within each parcel (calculated on fMRIPREP output)
num_good_timepoints: the total number of good timepoints left after scrubbing and removing initial volumes
std_after_regression: The temporal standard deviation of each parcel’s timesignal after nuisance regression (this is calcualated prior to the final filtering of the signal)
std_before_regression: The temporal standard deviation of each parcel’s timesignal prior to nuisance regression (if hpf_before_regression is used, this is calculated after that filtering step)
- std_regression_statistics
mean_remaining_std_ratio: the average of std_before_regression/std_after_regression across all parcels
least_remaining_std_ratio: the minimum of std_before_regression/std_after_regression across all parcels
In totallity, processing follows the sequence below: 1. Calculate DVARS on the input time-series. 2. If hpf_before_regression is used, filter the parcellated time-series, and the signals specified by clean_comps_dict, and noise_comps_dict. 3. Calculate the temporal standard deviation for each parcel (for std_before_regression) 3. Fit the signals generated from clean_comps_dict and noise_comps_dict to the parcellated timeseries (using only defined, not scrubbed points) and remove the signal explained from the noise_comps_dict. 4. Calculate the temporal standard deviation for each parcel (for std_after_regression) 5. Interpolate over any scrubbed timepoints 6. Apply either highpass, lowpass, or bandpass filter if specified 7. Set all undefined timepoints to NaN 8. Calculate DVARS on the output time-series 9. Calculate remaining meta-data
Example¶
from discovery_imaging_utils import func_denoising
from discovery_imaging_utils import dictionary_utils
#Path to saved dictionary directory structure
#created from parc_ts_dict
path_to_parc_ts_dict = '/insert/name/of/path'
#Load the parcellated dictionary
parc_dict = dictionary_utils.load_dictionary(path_to_parc_ts_dict)
#Set the parameters for denoising
hpf_before_regression = False #don't filter variables before regression
scrub_criteria_dictionary = {'std_dvars' : 1.3, 'framewise_displacement' : 0.5} #scrub high dvars and fd timepoints
interpolation_method = 'spectral'
noise_comps_dict = {'wmcsfgsr' : False, 'motion_regs_twentyfour' : False} #regress white matter, csf, and gsr signal + 24 motion regressors
clean_comps_dict = False #Skip including variables whose signal should be preserved in denoising
high_pass = 0.01 #High pass filter cutoff at 0.01Hz
low_pass = 0.08 #Low pass filter cutoff at 0.08Hz
denoised_func_dict = denoise(parc_dict,
hpf_before_regression,
scrub_criteria_dictionary,
interpolation_method,
noise_comps_dict,
clean_comps_dict,
high_pass,
low_pass)
#Save the output for later use
output_path = '/path/to/directory/to/be/created/for/output'
dictionary_utils.save_dictionary(denoise_func_dict, output_path)


public class FeatureSet
extends java.lang.Object
FeatureTrack
s associated with some audio data. FeatureSet provides methods for
reading and writing feature data to/from files.| Constructor and Description |
|---|
FeatureSet()
Instantiates a new empty FeatureSet.
|
FeatureSet(java.io.File file)
Instantiates a new FeatureSet from the given file.
|
| Modifier and Type | Method and Description |
|---|---|
void |
add(java.lang.String trackName,
FeatureTrack track)
Adds the given
FeatureTrack with the given name, writing over a previously stored FeatureTrack with the same name. |
void |
addGlobal(java.lang.String s,
java.lang.Object f)
Adds a set of features with the given name to the global features.
|
boolean |
contains(java.lang.String trackName)
Returns true if this FeatureSet stores a track with the given name.
|
boolean |
containsGlobal(java.lang.String feature)
Returns true if this FeatureSet stores a global feature with the given name.
|
static FeatureSet |
forSample(Sample s)
Tries to locate the FeatureSet for the given
Sample . |
FeatureTrack |
get(java.lang.String trackName)
Gets the
FeatureTrack with the given name. |
java.lang.Object |
getGlobal(java.lang.String s)
Gets the global features for the given name.
|
void |
printGlobalFeatures() |
void |
refresh()
Rereads the data from the stored file.
|
java.util.Map<java.lang.String,FeatureTrack> |
tracks()
Returns the tracks.
|
void |
write()
Writes to a file.
|
void |
write(java.io.File file)
Writes the data to the given
File and keeps the file ref for future use. |
void |
write(java.lang.String fn)
Writes the data to the named file, and keeps a file ref for future use.
|
public FeatureSet()
public FeatureSet(java.io.File file)
file
- the File.public static FeatureSet forSample(Sample s)
Sample
. Assumes that the features are stored in a file next to the Sample's file
but with the ending ".features".s
- the Samplepublic FeatureTrack get(java.lang.String trackName)
FeatureTrack
with the given name.trackName
- the track name.public void add(java.lang.String trackName, FeatureTrack track)
FeatureTrack
with the given name, writing over a previously stored FeatureTrack
with the same name.trackName
- the track name.track
- the track.public boolean contains(java.lang.String trackName)
trackName
- name to check.public void addGlobal(java.lang.String s, java.lang.Object f)
s
- the name used to identify the feature set.f
- the features.public java.lang.Object getGlobal(java.lang.String s)
s
- the name.public boolean containsGlobal(java.lang.String feature)
feature
- name to check.public void write()
FeatureSet
.public void refresh()
public void write(java.io.File file)
File
and keeps the file ref for future use.file
- the file.public void write(java.lang.String fn)
fn
- the file name.public java.util.Map<java.lang.String,FeatureTrack> tracks()
public void printGlobalFeatures()


Merge alignment data from a SAM or BAM with data in an unmapped BAM file.
java -jar picard.jar MergeBamAlignment \\ ALIGNED=aligned.bam \\ UNMAPPED=unmapped.bam \\ O=merge_alignments.bam \\ R=reference_sequence.fasta
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Arguments | |||
| --OUTPUT -O |
Merged SAM or BAM file to write to. | ||
| --REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
| --UNMAPPED_BAM -UNMAPPED |
Original SAM or BAM file of unmapped reads, which must be in queryname order. Reads MUST be unmapped. | ||
| Optional Tool Arguments | |||
| --ADD_MATE_CIGAR -MC |
true | Adds the mate CIGAR tag (MC) if true, does not if false. | |
| --ALIGNED_BAM -ALIGNED |
SAM or BAM file(s) with alignment data. | ||
| --ALIGNED_READS_ONLY |
false | Whether to output only aligned reads. | |
| --ALIGNER_PROPER_PAIR_FLAGS |
false | Use the aligner's idea of what a proper pair is rather than computing in this program. | |
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --ATTRIBUTES_TO_REMOVE |
Attributes from the alignment record that should be removed when merging. This overrides ATTRIBUTES_TO_RETAIN if they share common tags. | ||
| --ATTRIBUTES_TO_RETAIN |
Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging. | ||
| --ATTRIBUTES_TO_REVERSE -RV |
[OQ, U2] | Attributes on negative strand reads that need to be reversed. | |
| --ATTRIBUTES_TO_REVERSE_COMPLEMENT -RC |
[E2, SQ] | Attributes on negative strand reads that need to be reverse complemented. | |
| --CLIP_ADAPTERS |
true | Whether to clip adapters where identified. | |
| --CLIP_OVERLAPPING_READS |
true | For paired reads, clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate. Reads are first soft clipped so that the 3' aligned end of each read does not extend past the 5' aligned end of its mate. If HARD_CLIP_OVERLAPPING_READS is also true, then reads are additionally hard clipped so that the 3' unclipped end of each read does not extend past the 5' unclipped end of its mate. Hard clipped bases and their qualities are stored in the XB and XQ tags, respectively. | |
| --EXPECTED_ORIENTATIONS -ORIENTATIONS |
The expected orientation of proper read pairs. Replaces JUMP_SIZE | ||
| --HARD_CLIP_OVERLAPPING_READS |
false | If true, hard clipping will be applied to overlapping reads. By default, soft clipping is used. | |
| --help -h |
false | display the help message | |
| --INCLUDE_SECONDARY_ALIGNMENTS |
true | If false, do not write secondary alignments to output. | |
| --IS_BISULFITE_SEQUENCE |
false | Whether the lane is bisulfite sequence (used when calculating the NM tag). | |
| --MATCHING_DICTIONARY_TAGS |
[M5, LN] | List of Sequence Records tags that must be equal (if present) in the reference dictionary and in the aligned file. Mismatching tags will cause an error if in this list, and a warning otherwise. | |
| --MAX_INSERTIONS_OR_DELETIONS -MAX_GAPS |
1 | The maximum number of insertions or deletions permitted for an alignment to be included. Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. | |
| --MIN_UNCLIPPED_BASES |
32 | If UNMAP_CONTAMINANT_READS is set, require this many unclipped bases or else the read will be marked as contaminant. | |
| --PRIMARY_ALIGNMENT_STRATEGY |
BestMapq | Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragment, and none are marked as primary, more than one is marked as primary, or the primary alignment is filtered out for some reason. For all strategies, ties are resolved arbitrarily. | |
| --PROGRAM_GROUP_COMMAND_LINE -PG_COMMAND |
The command line of the program group (if not supplied by the aligned file). | ||
| --PROGRAM_GROUP_NAME -PG_NAME |
The name of the program group (if not supplied by the aligned file). | ||
| --PROGRAM_GROUP_VERSION -PG_VERSION |
The version of the program group (if not supplied by the aligned file). | ||
| --PROGRAM_RECORD_ID -PG |
The program group ID of the aligner (if not supplied by the aligned file). | ||
| --READ1_ALIGNED_BAM -R1_ALIGNED |
SAM or BAM file(s) with alignment data from the first read of a pair. | ||
| --READ1_TRIM -R1_TRIM |
0 | The number of bases trimmed from the beginning of read 1 prior to alignment | |
| --READ2_ALIGNED_BAM -R2_ALIGNED |
SAM or BAM file(s) with alignment data from the second read of a pair. | ||
| --READ2_TRIM -R2_TRIM |
0 | The number of bases trimmed from the beginning of read 2 prior to alignment | |
| --SORT_ORDER -SO |
coordinate | The order in which the merged reads should be output. | |
| --UNMAP_CONTAMINANT_READS -UNMAP_CONTAM |
false | Detect reads originating from foreign organisms (e.g. bacterial DNA in a non-bacterial sample),and unmap + label those reads accordingly. | |
| --UNMAPPED_READ_STRATEGY |
DO_NOT_CHANGE | How to deal with alignment information in reads that are being unmapped (e.g. due to cross-species contamination.) Currently ignored unless UNMAP_CONTAMINANT_READS = true. Note that the DO_NOT_CHANGE strategy will actually reset the cigar and set the mapping quality on unmapped reads since otherwisethe result will be an invalid record. To force no change use the DO_NOT_CHANGE_INVALID strategy. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --ADD_PG_TAG_TO_READS |
true | Add PG tag to each read in a SAM or BAM | |
| --COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
| --CREATE_INDEX |
false | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
| --CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
| --GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
| --MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --TMP_DIR |
One or more directories with space available to be used by this program for temporary storage of working files | ||
| --USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
| --USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
| --VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --VERBOSITY |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --showHidden |
false | display hidden arguments | |
| Deprecated Arguments | |||
| --JUMP_SIZE -JUMP |
The expected jump size (required if this is a jumping library). Deprecated. Use EXPECTED_ORIENTATIONS instead | ||
| --PAIRED_RUN -PE |
true | DEPRECATED. This argument is ignored and will be removed. |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Adds the mate CIGAR tag (MC) if true, does not if false.
Boolean true
Add PG tag to each read in a SAM or BAM
boolean true
SAM or BAM file(s) with alignment data.
Exclusion: This argument cannot be used at the same time as READ1_ALIGNED_BAM, READ2_ALIGNED_BAM
.
List[File] []
Whether to output only aligned reads.
boolean false
Use the aligner's idea of what a proper pair is rather than computing in this program.
boolean false
read one or more arguments files and add them to the command line
List[File] []
Attributes from the alignment record that should be removed when merging. This overrides ATTRIBUTES_TO_RETAIN if they share common tags.
List[String] []
Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging.
List[String] []
Attributes on negative strand reads that need to be reversed.
Set[String] [OQ, U2]
Attributes on negative strand reads that need to be reverse complemented.
Set[String] [E2, SQ]
Whether to clip adapters where identified.
boolean true
For paired reads, clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate. Reads are first soft clipped so that the 3' aligned end of each read does not extend past the 5' aligned end of its mate. If HARD_CLIP_OVERLAPPING_READS is also true, then reads are additionally hard clipped so that the 3' unclipped end of each read does not extend past the 5' unclipped end of its mate. Hard clipped bases and their qualities are stored in the XB and XQ tags, respectively.
boolean true
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
The expected orientation of proper read pairs. Replaces JUMP_SIZE
Exclusion: This argument cannot be used at the same time as JUMP_SIZE
.
The --EXPECTED_ORIENTATIONS argument is an enumerated type (List[PairOrientation]), which can have one of the following values:
List[PairOrientation] []
Google Genomics API client_secrets.json file path.
String client_secrets.json
If true, hard clipping will be applied to overlapping reads. By default, soft clipping is used.
boolean false
display the help message
boolean false
If false, do not write secondary alignments to output.
boolean true
Whether the lane is bisulfite sequence (used when calculating the NM tag).
boolean false
The expected jump size (required if this is a jumping library). Deprecated. Use EXPECTED_ORIENTATIONS instead
Exclusion: This argument cannot be used at the same time as EXPECTED_ORIENTATIONS
.
Integer null
List of Sequence Records tags that must be equal (if present) in the reference dictionary and in the aligned file. Mismatching tags will cause an error if in this list, and a warning otherwise.
List[String] [M5, LN]
The maximum number of insertions or deletions permitted for an alignment to be included. Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions.
int 1 [ [ -∞ ∞ ] ]
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
If UNMAP_CONTAMINANT_READS is set, require this many unclipped bases or else the read will be marked as contaminant.
int 32 [ [ -∞ ∞ ] ]
Merged SAM or BAM file to write to.
R File null
DEPRECATED. This argument is ignored and will be removed.
Boolean true
Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragment, and none are marked as primary, more than one is marked as primary, or the primary alignment is filtered out for some reason. For all strategies, ties are resolved arbitrarily.
The --PRIMARY_ALIGNMENT_STRATEGY argument is an enumerated type (PrimaryAlignmentStrategy), which can have one of the following values:
PrimaryAlignmentStrategy BestMapq
The command line of the program group (if not supplied by the aligned file).
String null
The name of the program group (if not supplied by the aligned file).
String null
The version of the program group (if not supplied by the aligned file).
String null
The program group ID of the aligner (if not supplied by the aligned file).
String null
Whether to suppress job-summary info on System.err.
Boolean false
SAM or BAM file(s) with alignment data from the first read of a pair.
Exclusion: This argument cannot be used at the same time as ALIGNED_BAM
.
List[File] []
The number of bases trimmed from the beginning of read 1 prior to alignment
int 0 [ [ -∞ ∞ ] ]
SAM or BAM file(s) with alignment data from the second read of a pair.
Exclusion: This argument cannot be used at the same time as ALIGNED_BAM
.
List[File] []
The number of bases trimmed from the beginning of read 2 prior to alignment
int 0 [ [ -∞ ∞ ] ]
Reference sequence file.
R File null
display hidden arguments
boolean false
The order in which the merged reads should be output.
The --SORT_ORDER argument is an enumerated type (SortOrder), which can have one of the following values:
SortOrder coordinate
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
Detect reads originating from foreign organisms (e.g. bacterial DNA in a non-bacterial sample),and unmap + label those reads accordingly.
boolean false
Original SAM or BAM file of unmapped reads, which must be in queryname order. Reads MUST be unmapped.
R File null
How to deal with alignment information in reads that are being unmapped (e.g. due to cross-species contamination.) Currently ignored unless UNMAP_CONTAMINANT_READS = true. Note that the DO_NOT_CHANGE strategy will actually reset the cigar and set the mapping quality on unmapped reads since otherwisethe result will be an invalid record. To force no change use the DO_NOT_CHANGE_INVALID strategy.
The --UNMAPPED_READ_STRATEGY argument is an enumerated type (UnmappingReadStrategy), which can have one of the following values:
UnmappingReadStrategy DO_NOT_CHANGE
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency STRICT
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version <IP_ADDRESS> built at Wed, 18 Aug 2021 19:58:25 -0400.


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- Cookies. Cookies are simple text files stored by your web browser that provide a method of distinguishing among donors and visitors to the website. Emma's Hope uses cookies to identify your browser as you visit pages on the Emma's Hope website.
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Emma's Hope is based in the United States, and any information transmitted to us may be stored, accessed, or processed in the United States. Residents of some other countries, including residents of the European Union, should be aware that the laws of the United States do not offer the same protections as the laws of your home country.
How do we use information?
We collect information primarily to accept donations, complete our charitable projects, and provide you with information concerning our services and events. We also use information for internal purposes (to better understand our supporter network) and for analytical purposes (to respond to requests for information and to improve our website, donor base, and outreach). We may inform you of other purposes at the time that we collect some forms of information. For example, if you sign up for an event, we may collect your information to process your application.
With whom do we share information?
We do not trade, share, or sell information that you provide to us with other organizations who intend to use it only to market their products or services to you.
There may be instances in which we share your information with others. We may share your information, for example, as required by law, with law enforcement, to comply with legal process, to protect our legal rights, to protect the safety or security of a person, or to protect against fraud, criminal acts, or misconduct.
Our commitment to data security
To help prevent unauthorized access, maintain data accuracy, and ensure the correct use of information, we have put in place appropriate physical, electronic, and managerial procedures to safeguard and secure the information we collect. For example, we secure our machines with mandated encryption protocols to secure our donor/company data. We also use industry accepted tools and techniques such as SSL and two-factor authentication to protect against unauthorized access to our systems. Additionally, all sensitive information is stored in secure repositories in secure cloud-based, AES encrypted web apps.
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If you would like to access the data that we have received from you, or make corrections to it, you may contact us at the email or mailing addresses provided at the end of this policy.
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Changes to this privacy statement. We may modify this privacy policy from time to time. Any changes will be reflected on this website. If we make a material change to this policy, and need to apply it to personal information that you provided to us before the change was made, we will attempt to contact you and obtain your consent to the change.
Communicating with us. If we need, or are required to, contact you about the privacy or security of your information we may do so by telephone, email, or mail. If you have any questions, concerns, requests, or comments about privacy, you can contact us by email, telephone, or mail at:
<EMAIL_ADDRESS>+1<PHONE_NUMBER>
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Effective: May 24, 2018


“Panādo nāma so rājā,
yassa yūpo suvaṇṇayo;
Tiriyaṁ soḷasubbedho,
ubbhamāhu sahassadhā.
There was a king named Panāda
who had a sacrificial post all golden.
Its height was sixteen times its width,
and the top was a thousand-fold.
Sahassakaṇḍo satageṇḍu,
dhajālu haritāmayo;
Anaccuṁ tattha gandhabbā,
chasahassāni sattadhā”ti.
… Bhaddajitthero ….
It had a thousand panels and a hundred ball-caps,
all adorned with banners, and made of gold.
There danced the fairies,
numbering seven times six thousand.


Welcome to my portfolio! Below you can find a list of the projects I've created in my time as a developer.
Some artwork of me created by my cousin Zach Wilson
My name is Jacob Wilson, I live in Anchorage, Ak but was born and raised in Portland, Or. I have had an interest in developement since highschool but didn't start working towards becoming one until fall of summer of 2020. My origional intention was to learn what it took to become a game developer, but along the way I developed a love for coding!
I've worked many jobs in many different titles including: security, retail, fuel clerk, pizza delivery, and janitor. When covid hit and I was given the oppertunity to work on something more inline with who I am I started teaching myself to code so I could pursue a carrier in game developement.


Last updated: 2021-07-03
Checks: 7 0
Knit directory: wildlife-bacteria/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | af6ad5b | siobhon-egan | 2021-07-03 | general update |
ozmaps
Create map of study sites using ozmaps
package and associated data package for subdivision of regions.
Link to useful tutorial in the ggplot2 book here.
Load packages
#ozmaps data not on CRAN
#devtools::install_github("mdsumner/ozmaps.data")
pkgs <- c("ozmaps", "sf", "sp", "dplyr", "rgdal",
"raster", "ggplot2", "viridis", "readr",
"paletteer", "rmapshaper", "ggrepel",
"tidyverse", "ozmaps.data", "readxl")
lapply(pkgs, require, character.only = TRUE)
Import data
site_map <- read_excel("data/site_map.xlsx")
site_map_lab = column_to_rownames(site_map, var = "Site name")
Create large base map for Australia with study sites
oz_states <- ozmaps::ozmap_states
ggplot(oz_states) +
geom_sf() +
coord_sf()
oz_states <- ozmaps::ozmap_states %>% filter(NAME != "Other Territories")
oz_votes <- rmapshaper::ms_simplify(ozmaps::abs_ced)
ggplot() +
geom_sf(data = oz_states, mapping = aes(fill = NAME), show.legend = FALSE) +
geom_sf(data = oz_votes, fill = NA) +
coord_sf()
# large map
map1 = ggplot() +
geom_sf(data = oz_votes) +
geom_sf(data = oz_states, colour = "black", fill = "NA") +
geom_point(data = site_map_lab, mapping = aes(x = lon, y = lat, color = Site, shape=Site, size= 3)) +
coord_sf() + theme_classic() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank()) + xlim (114,155)
map1
Create insert maps for Perth and Sydney regions
# base map for inserts
map2 = ggplot() +
geom_sf(data = oz_votes) +
geom_sf(data = oz_states, colour = "black", fill = "NA") +
geom_point(data = site_map_lab, mapping = aes(x = lon, y = lat, color = Site, shape=Site, size= Size)) +
coord_sf() + theme_classic() + theme(legend.position = "none", axis.title.x = element_blank(), axis.title.y = element_blank())
# Sydney region
map3 = map2 + coord_sf(xlim = c(150, 152), ylim = c(-35, -33.0)) + theme(legend.position = "none") + theme(axis.title.x = element_blank(), axis.title.y = element_blank())
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
map3
# Perth region
map4 = map2 + coord_sf(xlim = c(115, 117), ylim = c(-32.5, -31)) + theme(legend.position = "none") + theme(axis.title.x = element_blank(), axis.title.y = element_blank())
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
map4
Save maps
ggsave("map_base.pdf", plot = map1, path = "output/plots", width = 30, height = 15, units = "cm")
ggsave("map_NSW.pdf", plot = map3, path = "output/plots", width = 10, height = 10, units = "cm")
ggsave("map_WA.pdf", plot = map4, path = "output/plots", width = 10, height = 10, units = "cm")
Capital cities for reference
oz_capitals <- tibble::tribble(
~city, ~lat, ~lon,
"Sydney", -33.8688, 151.2093,
"Melbourne", -37.8136, 144.9631,
"Brisbane", -27.4698, 153.0251,
"Adelaide", -34.9285, 138.6007,
"Perth", -31.9505, 115.8605,
"Hobart", -42.8821, 147.3272,
"Canberra", -35.2809, 149.1300,
"Darwin", -12.4634, 130.8456,
)
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 ozmaps.data_0.0.1 forcats_0.5.1 stringr_1.4.0
[5] purrr_0.3.4 tidyr_1.1.2 tibble_3.1.0 tidyverse_1.3.0
[9] ggrepel_0.9.1 rmapshaper_0.4.4 paletteer_1.3.0 readr_1.4.0
[13] viridis_0.5.1 viridisLite_0.3.0 ggplot2_3.3.3 raster_3.4-5
[17] rgdal_1.5-23 dplyr_1.0.5 sp_1.4-5 sf_0.9-7
[21] ozmaps_0.3.6 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.0 lubridate_1.7.10 httr_1.4.2 rprojroot_2.0.2
[5] tools_4.0.3 backports_1.2.1 bslib_<IP_ADDRESS>01 utf8_1.2.1
[9] R6_2.5.0 KernSmooth_2.23-18 lazyeval_0.2.2 rgeos_0.5-5
[13] DBI_1.1.1 colorspace_2.0-0 withr_2.4.1 tidyselect_1.1.0
[17] gridExtra_2.3 curl_4.3 compiler_4.0.3 git2r_0.28.0
[21] cli_2.3.1 rvest_0.3.6 geojsonsf_2.0.1 xml2_1.3.2
[25] sass_0.3.1 scales_1.1.1 classInt_0.4-3 digest_0.6.27
[29] foreign_0.8-81 rmarkdown_2.7.2 pkgconfig_2.0.3 htmltools_<IP_ADDRESS>
[33] highr_0.8 dbplyr_2.1.0 jsonvalidate_1.1.0 rlang_0.4.10
[37] rstudioapi_0.13 httpcode_0.3.0 jquerylib_0.1.3 generics_0.1.0
[41] farver_2.0.3 jsonlite_1.7.2 magrittr_2.0.1 Rcpp_1.0.6
[45] munsell_0.5.0 fansi_0.4.2 lifecycle_1.0.0 stringi_1.5.3
[49] whisker_0.4 yaml_2.2.1 jqr_1.2.0 oz_1.0-21
[53] maptools_1.0-2 grid_4.0.3 promises_<IP_ADDRESS> geojsonio_0.9.4
[57] crayon_1.4.1 lattice_0.20-41 haven_2.3.1 geojson_0.3.4
[61] hms_1.0.0 knitr_1.31 pillar_1.5.1 geojsonlint_0.4.0
[65] codetools_0.2-18 crul_1.1.0 reprex_1.0.0 glue_1.4.2
[69] evaluate_0.14 V8_3.4.0 modelr_0.1.8 vctrs_0.3.7
[73] httpuv_1.5.5 cellranger_1.1.0 gtable_0.3.0 rematch2_2.1.2
[77] assertthat_0.2.1 xfun_0.21 broom_0.7.5 e1071_1.7-4
[81] later_<IP_ADDRESS> class_7.3-18 units_0.7-0 ellipsis_0.3.1


STAY INFORMED: Check Live Doppler 7 Radar this winter weather season
by Breaking News StaffStay weather aware and prepared as severe weather affects the Miami Valley.
The free WHIO Weather App will keep you alert and informed of changing weather conditions, no matter where you are, at home or traveling on the road. You’ll be able to access a live radar anytime, anywhere. You’ll also receive weather watches and warnings no matter where you are.
Install the WHIO Weather App free now from the Google Play or Apple store. Right at your fingertips, you'll have access to:
- Live radar to track rain, lightning and storms
- School closings
- Hour-by-hour forecasts
- Hyper-local forecasts for your county
- Forecasts wherever you travel in the U.S.
HOW DO I ADD MY CITY OR LOCATION IN THE APP?
Once you have downloaded the app, it is time to setup the locations you would like to monitor. Remember, these can change whenever you'd like with a push of a button.
- In the WHIO Weather app, look for the three bars at the top left of your screen
- Click on “Settings” in the navigation
- Click on “Edit Locations” and then “Add Location”
- Type in the location(s) you are interested in saving and select from the dropdown
- Tap “DONE” in the upper right-hand corner
After that, you can save up to 10 locations by typing in the city and state. These locations can be anywhere you wish to receive weather updates.
SHOULD I "ENABLE" BACKGROUND TRACKING?
A new feature in the app is its ability to track storms even when the app isn't open and update you wherever you go...even out of state. If you travel into a location that is being impacted by weather, you will automatically be updated through the app.
- Once in the App, click the 'plus sign' at the top left of your screen
- Go to the Settings button at the bottom of your locations tab
- Click Background Tracking, this will take you to your phone's settings
- Make sure under the 'Location' option you chose 'always'
DO I HAVE TO BE ALERTED TO EVERYTHING WEATHER RELATED?
The WHIO Weather App is unique because it allows you to choose which the weather alerts for which you want to receive notifications. All watches, warnings and advisories that the National Weather Service issues are available in our app.
- Make sure there is a check by the alerts you want to receive
- You can turn off any notification you don't want by clicking the check mark
WHY DIDN'T THE WARNING GO OFF ON MY PHONE?
A special feature on the WHIO Weather App is the ability for the app to notify you ONLY when your GPS or saved locations are in the POLYGON for a warning. The National Weather Service draws polygons when it issues warnings and advisories.
WATCHES on the other hand are issued for entire counties, not polygons. If your location falls in a county where a watch is issued you WILL get an alert.
ISN'T THE 7-DAY JUST LIKE ANY OTHER WEATHER APP?
Unlike most apps that rely on a computer to just dump weather data on to their app, the StormCenter 7 Team updates the forecast on the WHIO Weather App each day, multiple times a day. With the WHIO Weather App you are getting a detailed forecast specifically created for the Miami Valley. It's not from a meteorologist many states away.
HOW DO I SEE THE LATEST LIST OF SCHOOL/ BUSINESS CLOSINGS AND DELAYS?
We've added the latest list of school and business closings and delays in the WHIO Weather App so you can check the list from wherever you're located. Simply open the app, along the bottom is a tool bar, 'Closings' is the third option from the left. This will take you directly to the most recently updated list. This new feature will better help you plan your day, allowing you to adjust as needed when your kids' school or your place of business issues a delay or closes due to road conditions or other reasons.
I MISSED A NEWSCAST, HOW CAN I GET MY FORECAST?
If you miss a TV newscast, you can still keep up with the latest video forecasts our meteorologists create throughout the day. These short weather video segments tell the weather story of the day, how it will impact you, and contain their scientific explanations for unique elements of the forecast you won't get in a written story or graphic. This is a great tool during severe weather days and when a big winter storm may impact the Miami Valley. These custom video forecasts created by the StormCenter7 team of Meteorologists can be found under the 'Video' tab.
WHAT CAN I SEE ON THE INTERACTIVE RADAR BESIDES RAIN AND SNOW?
The Interactive Radar is available year-round in the WHIO Weather App. Features on the app allow you to see lightning strikes along with satellite and radar. Under the 'Radar' tab you can click on the 'Layer' icon to overlay things like watches and warnings so you can see where storms and alerts are in relation to your location.


Google's Compact Language Detector 3 is a neural network model for language identification and the successor of 'cld2' (available from CRAN). The algorithm is still experimental and takes a novel approach to language detection with different properties and outcomes. It can be useful to combine this with the Bayesian classifier results from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
| Version: | 1.1 |
| Imports: | Rcpp |
| LinkingTo: | Rcpp |
| Suggests: | testthat, cld2 |
| Published: | 2018-06-28 |
| Author: | Jeroen Ooms [aut, cre], Google Inc [cph] (CLD3 C++ library) |
| Maintainer: | Jeroen Ooms <jeroen at berkeley.edu> |
| License: | Apache License 2.0 |
| URL: | https://github.com/ropensci/cld3 (devel) https://github.com/google/cld3 (upstream) |
| NeedsCompilation: | yes |
| SystemRequirements: | libprotobuf and protobuf-compiler |
| Materials: | NEWS |
| CRAN checks: | cld3 results |
| Reference manual: | cld3.pdf |
| Package source: | cld3_1.1.tar.gz |
| Windows binaries: | r-devel: cld3_1.1.zip, r-release: cld3_1.1.zip, r-oldrel: cld3_1.1.zip |
| OS X binaries: | r-release: cld3_1.1.tgz, r-oldrel: cld3_1.1.tgz |
| Old sources: | cld3 archive |
| Reverse suggests: | cld2 |
Please use the canonical form https://CRAN.R-project.org/package=cld3 to link to this page.


{% extends 'tenant_configuration/base.html' %} {% load staticfiles i18n compress thumbnail %} {% block content %} {% compress js inline %} {% include 'tenant_configuration/organization/3/js.html' %} {% endcompress %}
Now, we are going to set up tags to help you categorize your clients. These help you group your clients by a characteristic or program that you may offer. Tags will be a great help when it comes to searching for clients, analzying your data, and creating reports. The best part is that clients can have multiple tags, and tags can also be added or removed as often as needed. Not sure where to start? For example, you can use:
newcomers - this could help to designate clients that are new to the country and may require additional supports or services
spanish language - you could use any language as a tag here to indicate that the client (in this case) speaks Spanish
entrepreneurship 101 - if you were running a program called Entrepreneurship 101, then you could create this tag to designate someone as being part of a program.
Now, why don't you go ahead and create a few tags. You should add tags for any programs that you currently offer, or plan to offer in the next 3 months. We recommend that you choose 3 from the list below or create at least 3 to start. If you don't create any, the system autocreates a 'general intake' tag that you can use.


auth = req.HTTPBasicAuthHandler()
opener = req.build_opener(proxy, auth, req.HTTPHandler)
req.install_opener(opener)
return req.urlopen(getfile)
auth = req.HTTPBasicAuthHandler()
opener = req.build_opener(proxy, auth, req.HTTPHandler)
req.install_opener(opener)
response = req.urlopen(getfile + ".gz")
if "gzip" in response.info().get("Content-Type"):
buf = BytesIO(response.read())
response = gzip.GzipFile(fileobj=buf)
return response


Burning Bush
Descartes and Heidegger
This is an essay written for a modern philosophy course in my undergraduate
work which draws comparisions between two very different philosophers.
Critique of Hobbes
A critique of Thomas Hobbes and his trademark cynical view of human nature.


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A tiny (1838b minfied + gzipped) jQuery plugin for scrolljacking and auto-hashing
See it on GitHub, or see some comparisons
Try out other examples!
This section is not inside the section wrapper, so normal scrolling here!
Try swiping up, down, left or right on a touch device and see the colour of the coloured box change.
Try swiping up, down, left or right on a touch device and see the colour of the coloured box change.
Try swiping up, down, left or right on a touch device and see the colour of the coloured box change.
Try swiping up, down, left or right on a touch device and see the colour of the coloured box change.
Try swiping up, down, left or right on a touch device and see the colour of the coloured box change.
Try swiping up, down, left or right on a touch device and see the colour of the coloured box change.