At December 19, Saturn stand away Jupiter is about 13 arcminute, which we call the conjunction of Saturn and Jupiter. I point the 750mm telescope to southern west where Sun fall. It is the first time for me to see and capture them: Saturn, Jupiter and its moons. Form the layout of Jupiter’s moons, I’m happy to image that the moon’s orbit plane, Saturn ring, even the relative position of Sun, Earth, Saturn, Jupiter. I can feel where I’m in the Solar system. If I don’t try to capture it in person, I won’t find this kind of fun.

I’m very luck. First, the floor door in laboratory was opened which was always closed. Second, I captured them at December 19 rather after that, although only little time for me to do it after 19:00. After December 19, sky is filled with cloud in Shenzhen.

Photograph with tree silhouette is good. But it is better to choose tree more far away. I want to catch more moon, so I don’t aware that exposure is too long to see the Jupiter surface and Saturn ring. More, I don’t calibrate telescope’s light pathway, capture dark frame……

Note to calculate Field of View( F.O.V): $F.O.V = l/f$, where F.O.V is in rad, $l$ is the camera sensor size and $f$ is telescope focal length. Two telescope with Sony A7 full-frame(35.8mmx23.9mm), APS-C(23.6mmx15.7mm):

• Sky-Watcher DOB 16’, F1800mm: (23.9/1800)/(2pi/360)=0.76 degree
• Sky-Watcher Newtonian Reflector, 750mm: (23.9/750)/(2pi/360)=1.83 degree, 1.20 degree for APS-C.

Reference

• Photograph Tip from NASA
• https://en.wikipedia.org/wiki/Great_conjunction
• Jupiter-Saturn Conjunction Series from 0 CE to 3000 CE
• Calibrate Newtonian reflector

本地化 KStars

在十二月里，我大致翻译了 4815 个词。原 kstars.pot 约有词三万六未翻译，现还剩三万五。 得加快了！另外得找 Siyu 一起来干。

学到一点：专有名词可以查专业字典以及参考其他译作。主要参考了中国科学院国家天文台提 供的天文学名词数据库。

《语言小书》A Little Book of Language

戴维·克里斯特尔( David Crystal)著，郭曌宇译，广西师范出版社 关键词：词汇、发音、句子语法、拼写、词典

当人们积极地使用某些词时，我们把它们称为“积极词汇”(active vacabulary)。 但人们能理解某些词的意思却不会用时，我们把它们称为“消极词汇”(passive vocabulary)。

方言的差异主要体现在词汇和语法上。口音只和发音有关。它们都 能告诉我们人们从何而来。

词典的作用：释意、发音。词典需要时常更新。

第四十章：你们的语言世界

1. 世界上许多语言正在消亡，我希望你们能关注这个问题。
2. 我希望你们能关注少数族裔的语言，哪怕它们还没走到岌岌可危的地步。
3. 我希望你们能重视语言，有学习各种语言的欲望。
4. 我希望你们关注自己母语的多样性。
5. 我希望你们能关注自己母语中的各种风格。
6. 我希望你们能关心那些在学习和使用母语方面有障碍的人们，并尽可能帮助他们。

确实只是一本小书：让我感受到人如何说话、保护语言的重要，同时推着我去看更多 的书，更深入地学习。我慢慢感觉到我一直没有好好去听别人怎么说话，而是把别人话 大致“拟合”到我的理解。我开始仔细听别人说话，像婴儿一般感受、学习发音，思考如何组织 用词和句子。努力理解“话是怎么被说出来的”。

语言考试

想解决语言考试的老大难问题。原想能准备好，月末去考试。找一个早上，尝试做了 GRE 的 Verbal 和 Quant。一半不到的正确率。看不懂的单词一堆，连 LAB 的讲解也不能全懂。

《英汉翻译教程》A Course in English-Chinese Translation

严复：“译事三难：信、达、雅。求其信，已大难矣！顾其信，不达，虽译，犹不译也，则达尚焉…… 至原文词理本深，难于共喻，则单前后引衬，以显其意，凡此经营，皆所以为达，为达即所以为 信也。” —- 《天演论-译例言》

马建忠的善译三大要求：第一、译者首先要对两种语言素有研究，熟知彼此的异同；第二、弄清原文 的意义、精神和语气，把它传达出来；第三、译文与原文毫无出入，“译成之文，适如其所译。” —-《拟投翻译书院议》

鲁迅：“凡是翻译，必须兼顾着两面，一当然力求其易解，一则保存着原作的风资。”

词类转换：英语句子中往往只有一个谓语动词，而汉语中则可以好几个动词连用。同时英语中有大量 动词派生的名词和具有动作意义的名词，这些名词可转译成汉语动词。另一方面，英语中许多名词 派生的动词，不易找到相对应的汉语名词，这时可以转译成汉语名词。

增词、重复、省略词汇：按照意义（或修辞上）和句法上的需要增加一些词来更忠实地表达原思想内容。 有时为了明确、强调或生动，往往需要将一些关键性的词加以重复。省略是删掉一些可有可无的，或者 有了反嫌累赘或违反译文语言习惯的词。

He was thin and haggard and he looked miserable.
他消瘦憔悴，（……）看上去一副可怜相。

We live and lean.
（……）活到老，学到老。

翻译的过程：大体上可分为理解、表达和校核三个阶段。

其他未竟之事

• 王力的汉语语法
• 英译中的方法和技巧
• 英语的语法和音标

最后更新: 20210207

用 Eqmod 代替 SynScan 手柄

好处是，不用接手柄，少一条线，而且不用手动输入地理座标和时间。 觉得便于 Kstars 的 Alignment 和解析。

调节齿轮和轴承的耦合

1. 发现调好齿轮耦合后，接 type-c 充电头，红色的 LED 不闪了；但接 充电宝，依然闪。
2. 应该先调斜面齿轮的咬合，使锁死赤经、赤纬轴后，两轴都没有空程。 然后从大到小调电机传动齿轮咬合。

https://zhuanlan.zhihu.com/p/59925522

Thanks for my friends and SUSTech who enable me to acess to following resouces.

A 350mm telescope(SkyRover 70SA), a Sky-Watcher HEQ5 Pro mount, a Sony 7a DSLR, a 190mm guide scope and QHY-5FIIM guiding camera. Kstars controls all these devices to capture sky with a raspberry pi 4B.

Most of galaxies is very dark. I want to capture the color of galaxy, so I need to exposure in a long time, such as 10 minutes. A mount is required to follow movement of stars.

Alignment

Use eqmod to control HEQ5 instead of hand controller. Why align coordinates, then do polar alignment?

https://www.myastroscience.com/polaralignment Tutorial on How To Align Polar Scope to RA axis of your mount

Use KStars polar alignment assistant. Tutorial see Youtube Correct vector.

RED LED Starry: Motor First upside down, then motor bonding

Guiding

At KStars, set camera to QHY5-LL-M, source to EQMod. At the begin, I set source to camera, which cause short drift error. Due to camera don’t connect to mount directly.

Imaging

Flat field: ISO don’t effect. The color should do nothing.[8] T-shirt Dark field: Temperature cause dark current. It should be same time as light frame. Bias field: readout noise and bias

LRGB filter

Pre-processing, Registration, Stacking

Indeed, pre-processing images with Dark, Bias and Flat do not remove noise but unwanted signal.

calibrated image = $frac{light-masterDark-masterBias}{masterFlat-masterFlatDark-masterBias}$

Shot noise obey poisson distribution. SNR

Sigma Clipping is an rejection algorithm. At each iteration, the central value and dispersion (or sigma) of the pixel stack are estimated, and all pixels whose distances from the central value are larger than a prescribed value in sigma units are rejected. Winsorization, named after statistician Charles P. Winsor, is a process for robust estimation of sample parameters in presence of outliers.

Reference from Pixinisight and free-astro.

Ref: https://free-astro.org/index.php?title=Siril:Tutorial_preprocessing

PC setting

Compile and install indi.

Power

For power support unit, I choose bacterial. It need to consider: total capacity, maximum power, supported voltage, weight, charging method, recharge cycle, battery material.

Now I’m using a charging pocket: 187Wh, 12V/3A.

In order to make most use of old charging pocket, how can I combine multiple battery and keep constant output?

Single Image Processing

Background extraction: When an image contains an intense light pollution, it is useful to remove it. Siril provides a “Background Extraction” tool in order to remove the gradient of the sky background. Siril uses a polynomial up to the fourth degree. The 4th degree polynomial is generally a good choice, for this model, though the tool allows for first to fourth degree.
Ref:https://free-astro.org/index.php?title=Siril:Manual

Color calibration, Histogram transfer, Remove green noise.

Last upadte: 20210228

Reference

1. https://www.myastroscience.com/
2. https://pixls.us/articles/processing-a-nightscape-in-siril/
3. http://www.astrosurf.com/comolli/flatfield2.htm
4. https://www.rc-astro.com/index.php
5. http://www.stargazing.net/David/QSI/ccdperfflats.html
6. http://www.renzodelrosso.com/utilita/flatbox.htm
7. https://www.zhihu.com/column/HGAstronomyStudio
8. https://zhuanlan.zhihu.com/p/57265735
9. https://crazygame12345.wordpress.com/tutorial/
10. http://www.astro-imaging.com/Tutorials.html
11. https://www.youtube.com/watch?v=qYXd0rrAzjg

The error logs about touchscreen are:

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[hf@surface ~]$ dmesg | grep silead
[   14.568268] silead_ts i2c-MSSL1680:00: supply vddio not found, using dummy regulator
[   14.568326] silead_ts i2c-MSSL1680:00: supply avdd not found, using dummy regulator
[   14.571859] silead_ts i2c-MSSL1680:00: Silead chip ID: 0x80360000
[   14.716552] silead_ts i2c-MSSL1680:00: Direct firmware load for silead/mssl1680.fw failed with error -2
[   14.716562] silead_ts i2c-MSSL1680:00: Firmware request error -2
[   14.898341] silead_ts: probe of i2c-MSSL1680:00 failed with error -2

Touchscreen driver is already installed, but lack of responding firmware. At the begin, I install the compiled firmwares from AUR:gsl-firmware-git and copy gsl1680-chuwi-hi10-air.fw to mmsl1680.fw. This firmware is able to driver touchscreen, but fail to calibration which seems to wrong hardware information are contained.

So, I extract firmware from windows firmware. Then just work! But calibration only work in X11 gnome but not Xwayland, because I have no idea Xwayland configration file.

Note: press F7 to choose boot device

Reference:

• https://hackaday.io/project/83212-liberating-a-50-windows-tablet/log/116445-testing-the-touchscreen
• https://github.com/onitake/gsl-firmware
• https://www.jianshu.com/p/b1d1f681dee6
• https://wiki.archlinux.org/index.php/Calibrating_Touchscreen#Your_screen
• https://wiki.archlinux.org/index.php/Touchscreen

一对母女游完泳，走在路上。女儿转过头对妈妈说：“这棵树上长了一棵小树”。

八月的正午，俩年轻的妈妈，各自带着儿子过马路。其一个男孩对另一个男孩 放声说，“你叫我大哥，我叫你小哥”。“大哥大哥大哥”，“小哥小哥小哥” 和 妈妈们的笑声，让夏日的空气变得轻盈透彻。

周末，徒步装扮的一家走在集悦城门口。哥哥问妹妹，“妈煮一个鸡蛋五分钟， 那煮十个鸡蛋多少分钟？”妹妹说，“五分钟”。爸爸笑说，“错，十分钟”。妹妹 说，”可以一起煮“

深圳音乐厅外，年轻爸爸带着小不点女儿。
爸爸：卖些小东西
女儿：什么是小东西
爸爸：饮料啊
女儿：什么是饮料
爸爸：……<

师姐和她女儿一起包场看电影。女儿：好可怕啊，我要所有所有人陪我一起看。

一次春天，师姐女儿从北方来深圳，看着落叶，对师姐说：凭什么这样？春天 凭什么掉叶子！

妈：酸奶给我喝一点好吗？
女儿：不给
妈：那酸奶是谁买的？
女儿：妈妈
妈：你爱妈妈吗？
女儿：爱
妈：给我酸奶喝吗？
女儿：不

深圳刚入秋，大风的早晨。背着书包的儿子：妈，能不能让我蹲着走路？

“为什么小朋友都喜欢白色的棋子，只有七哥喜欢黑色？我们能一起用一种颜色吗”

早上面包房，小女孩拿起塑料袋最后扯剩下的耳朵。妈妈：捡这东西干嘛？女儿： 这是小抹布，拿回家…

中国古代称彗星、新星或超新星称为客星，所以说有“客”自远方来。

用Sony A7 和 裕众的 70SA Pro(70mm, F/5) 大致从晚上九点拍到10点。

拉伸对比度后，我做成了一个延时视频(从这下载)。

其他同好的记录： http://www.astrocn.com/beta/archives/3591

我想记下时代和岁月留给老人的痕迹

熟过头的蕉仔

老伯手拿一把香蕉，走过大门口，在天井叫着爷爷。爷爷耳朵不好，老伯叫了几声，没听到 回应。老伯转头出门，才看到爷爷从门外过来。老伯问，要这些蕉仔吗？说要我拿我去喂鸡。 爷爷回答，唔要，唔想吃。这些蕉仔熟过头了。看到老伯走出门口，往阿十婆那走。阿十婆 平日一人生活。穿过树叶，看到老伯和阿十婆在说话。希望阿十婆拿走了蕉仔。

老一辈口中的家乡话里有些生动，有趣，优美的短语，语言习惯。我想记下方言里优美的用 法，以免少说家乡话后，用词和用法只能从普通话翻译。

一撒雨：指雨下得很小或只下了一小会
泥都抠起来了：土表泥土干裂
田绳：田垄、田沿
烘：热
起睡：起床
生争：口角、争吵
着味：入味

Recently, I work on analysing large fluorescence microscope image. I want to use laboratory computers while are Windows-installation but free. To minimize hardware change, I boot linux kernel from a USB key, and mount root from NFS. Compared with fully diskless system which loads linux kernel from other TFTP, booting from USB Key are much easier to use in different computer without extra network setting. Finally, when I need to more computation power, I just power off non-busy computers, then booting from USB key.

I almost follow fedora magazine’s post How to Build a Netboot Server and this to solve password issue. We need to set server and client. In server( just a running fedora for daily use), I export a NFS for diskless system root folder.

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sudo dnf install -y nfs-utils
mkdir /firefly
echo "/friefly -fsid=0,rw,sec=sys,root_squash" > /etc/exports
# I don't close SELinux, but nfs still work
# add an exception for NFS service
firewall-cmd --add-service nfs
firewall-cmd --runtime-to-permanent
exportsfs -vr
systemctl enable nfs-server.service
systemctl start nfs-server.service

Then we just install a minimal system image into NFS folder.

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sudo -i
dnf -y --releasever=32 --installroot=/firefly install fedora-release systemd\
passwd rootfiles sudo dracut dracut-network nfs-utils vim-minimal dnf

We disable hostonly mode so that the initramfs image will work on a wider set of hardware platforms and we need to add support for networking and NFS.

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echo 'hostonly=no' > /firefly/etc/dracut.conf.d/hostonly.conf
echo 'add_dracutmodules+=" network nfs "' > /firefly/etc/dracut.conf.d/netboot.conf
dnf -y --installroot=/firefly install kernel

Other configures

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#Disable logging to the console:
echo 'kernel.printk = 0 4 1 7' > /firefly/etc/sysctl.d/00-printk.conf
MY_CLIENT_HOSTNAME=firefly
echo $MY_CLIENT_HOSTNAME > /firefly/etc/hostname

I don’t follow fedora magazine post to set read-only mode and use RAM as storage. I want my diskless system keep all changes.

I was trouble in password error for many days at the first time: password update fail and never match new password. I mistake to use ro parameter in NFS, which export a read-only NFS. Another mistake is SELinux issues, which cause failure to reset password.

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restorecon /firefly/etc/passwd* /firefly/usr/bin/passwd
sudo systemd-nspawn -D /firefly sh -c "
# Set root password to fedora and create user fedora.
yes fedora | passwd
useradd -m -s /bin/bash fedora
yes fedora | passwd fedora

Now, we can prepare to create boot loader using iPXE. Download and compile iPXE.

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git clone http://git.ipxe.org/ipxe.git $HOME/ipxe
# create a special startup script for our bootloader:
cat << 'END' > $HOME/ipxe/init.ipxe
#!ipxe

prompt --key 0x02 --timeout 2000 Press Ctrl-B for the iPXE command line... && shell ||

dhcp || exit
set prefix file:///linux
chain ${prefix}/boot.cfg || exit
END
# Enable the “file” download protocol:
echo '#define DOWNLOAD_PROTO_FILE' > $HOME/ipxe/src/config/local/general.h
# Buld the boot loader
sudo dnf groupinstall -y "C Development Tools and Libraries"
cd $HOME/ipxe/src
make clean
make bin-x86_64-efi/ipxe.efi EMBED=../init.ipxe
# You should build it in an UEFI system. I fail to build in a BIOS system.

Then copy boot loader and kernel image to an FAT16/32 formatted USB Key.

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IPXE_FILE="$HOME/ipxe/src/bin-x86_64-efi/ipxe.efi"
mkdir -p $HOME/esp/efi/boot
mkdir $HOME/esp/linux
cp $IPXE_FILE $HOME/esp/efi/boot/bootx64.efi
DEFAULT_VER=$(ls -c /firefly/lib/modules | head -n 1)
MY_DNS1=x.x.x.x
MY_DNS2=x.x.x.x
MY_NFS4=sword.xxx.xxx
cat << END > $HOME/esp/linux/boot.cfg
#!ipxe

kernel --name kernel.efi \${prefix}/vmlinuz-$DEFAULT_VER initrd=initrd.img ro ip=dhcp rd.peerdns=0 nameserver=$MY_DNS1 nameserver=$MY_DNS2 root=nfs4:$MY_NFS4:/firefly console=tty0 console=ttyS0,115200n8 audit=0 selinux=0 quiet
initrd --name initrd.img \${prefix}/initramfs-$DEFAULT_VER.img
boot || exit
END

#Copy the Linux kernel and its associated initramfs
cp $(find /fc28/lib/modules -maxdepth 2 -name 'vmlinuz' | grep -m 1 $DEFAULT_VER) $HOME/esp/linux/vmlinuz-$DEFAULT_VER
cp $(find /fc28/boot -name 'init*' | grep -m 1 $DEFAULT_VER) $HOME/esp/linux/initramfs-$DEFAULT_VER.img

Our resulting directory layout should look like this, and we need to copy all files inside esp into EFI system partition on USB Key:

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esp/
├── efi
│   └── boot
│       └── bootx64.efi
└── linux
    ├── boot.cfg
    ├── initramfs-5.6.11-300.fc32.x86_64.img
    ├── initramfs-5.6.13-300.fc32.x86_64.img
    ├── vmlinuz-5.6.11-300.fc32.x86_64
    └── vmlinuz-5.6.13-300.fc32.x86_64

3 directories, 6 files

At the end, boot your USB key and have a lots of fun.

More reading:

https://docs.fedoraproject.org/en-US/Fedora/14/html/Storage_Administration_Guide/nfs https://wiki.gentoo.org/wiki/Diskless_nodes/zh-cn

Target: Passthrough SAS HBA( LSI SAS3008 PCI-Express Fusion-MPT SAS-3) and HP410i raid controller to Proxmox VM.

ISSUE: SAS HBA fail to passthrough to Promox VM, and it show following error in Proxmox shell:

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vfio: failed to set iommu for container: Operation not permitted
dmesg | grep -e DMAR -e IOMMU
vfio-pci 0000:0X:YY.Z: Device is ineligible for IOMMU domain attach due to platform RMRR requirement.  Contact your platform vendor.

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58.606116] DMAR: DRHD: handling fault status reg 2
[   58.606158] DMAR: [DMA Write] Request device [04:00.0] PASID ffffffff fault addr ffeee000 [fault reason 05] PTE Write access is not set
[  102.466175] DMAR: DRHD: handling fault status reg 102
[  102.466240] DMAR: [DMA Read] Request device [04:00.0] PASID ffffffff fault addr c763e000 [fault reason 06] PTE Read access is not set

Troubleshooting: HP ML350 G6 enables RMRR in PCIe slot, but linux kernel disables RMRR feature for performance issues.

HP ML350 G6 can’t disable RMRR by method as here and these, so I patch and compile kernel following Feni’s tutorial. After each kernel update, I have to compile again. You can follow the least tutorial.

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# install dependences
apt-get install git screen patch fakeroot build-essential devscripts libncurses5 \
libncurses5-dev libssl-dev bc flex bison libelf-dev libaudit-dev libgtk2.0-dev \
libperl-dev asciidoc xmlto gnupg gnupg2 rsync lintian debhelper libdw-dev \
libnuma-dev libsplang2-dev sphinx-common asciidoc-base automake cpio dh-python \
file gcc kmod libiberty-dev libpve-common-perl libtool perl-modules \
python-minimal sed tar zlib1g-dev lz4

# clone pve-kernel
cd /usr/src/
git clone git://git.proxmox.com/git/pve-kernel.git
# to pull least kernel, you should use
# git fetch 
# git pull

Build patch following Feni’s option B

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# 1. download and extract remove_rmrr_check_v2.zip atteched tutorial
cp  remove_rmrr_check_v2.patch /usr/src/pve-kernel/patches/kernel/
vim  /usr/src/pve-kernel/debian/scripts/find-firmware.pl
# 2. comment out the fourth line from above with a # so that it looks as such:
#die "strange directory name: $dir" if $dir !~ m|^(.*/)?(5.\d.\d+\-\d+\-pve)(/+)?$|;
# 3. edit the control.in file located at /usr/src/pve-kernel so that the generated package is named differently. This prevents errors when updating an up to date vanilla install. Add -removermrr to the pve-kernel article so the line lookes like this:
# 4. give your system a nice identifier,
vim /usr/src/pve-kernel/Makefile
# edit the EXTRAVERSION line near the top of the Makefile and add this to the end:
removermrr
make clean
make
dpkg -i *.deb
reboot

update-initramfs -u update-grub

P410i ISSUE(WIP):

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[ 35.715620] dmar: DMAR:[DMA Write] Request device [07:00.0] fault addr ffee0000
[ 35.715620] DMAR:[fault reason 05] PTE Write access is not set

/etc/modprobe.d/blacklist.conf und darin: https://forum.proxmox.com/threads/hp-proliant-microserver-gen8-raidcontroller-hp-p410-passthrough-probleme.30547/#post-153784

To turn hp P410i to HBA model and passthrough it, ref to hpsahba and Enable IT mode on HP Smart Array P410i RAID card on HP DL380 Gen7 servers

Ref:

• Feni’s tutorial
• Proxmox Wiki Pass(e) PCI Passthrough
• Proxmox Wiki Pass Disk

I enjoy to have a Acer R13 chromebook for myself. I post what I drive chromebook to be a good notebook for writing and programming.

Zotero on ARM

Official compile guide will trouble in arm platform, but I find a AUR zotero-arm-bin to solve it. Simple download firefox.deb, Zotero-5.0.84_linux_x86.tar.bz2, zotero.desktop from AUR link. Then follow the PKGBUILD extract executable files and install icon and desktop file. Please note that, I install zotero at ~/bin/zotero. You try modify to your purposed directory.

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# Extract firebox.deb
ar x firefox.deb data.tar.xz
tar xf data.tar.xz ~/bin/firefox --strip-components=3 
# you can use standard directory or other you want
rm data.tar.xz
# Extract Zotero-5.0.84_linux_x86.tar.bz2
tar xf Zotero-5.0.84_linux_x86.tar.bz2 ~/bin/zotero
# Copy zotero icons to a standard location
cp ~/zoter/chrome/icon/default/default16.png /usr/share/icons/hicolor/16x16/apps/zotero.png
cp ~/zoter/chrome/icon/default/default32.png /usr/share/icons/hicolor/32x32/apps/zotero.png
cp ~/zoter/chrome/icon/default/default48.png /usr/share/icons/hicolor/48x48/apps/zotero.png
cp ~/zoter/chrome/icon/default/default256.png /usr/share/icons/hicolor/256x256/apps/zotero.png
# Disable APP update
sed -i '/pref("app.update.enabled", true);/c\pref("app.update.enabled", false);' ~/bin/zotero/defaults/preferences/prefs.js
# No need to keep a shell around when launching Zotero
sed -i -r 's/^("\$CALLDIR\/zotero-bin" -app "\$CALLDIR\/application.ini" "\$@")/exec \1/' ~/bin/zotero/zotero
# Remove poppler binaries
rm ~/bin/zotero/{pdftotext,pdfinfo}
# Replace Firefox binaries
rm ~/bin/zotero/**.{so,chk}
rm ~/bin/zotero/gtk/*
rm -r ~/bin/zotero/gmp-clearkey
rm ~/bin/{updater,minidump-analyzer}
cp ~/bin/firefox/*.{so,chk} ~/bin/zotero
cp ~/bin/firefox/gtk2/*.so ~/bin/zotero/gtk2
cp ~/bin/firefox/plugin-container ~/bin/zotero/plugin-container
cp ~/bin/firefox ~/bin/zotero/zotero-bin
cp ~/bin/firefox/dependentlibs.list ~/bin/zotero/dependentlibs.list
cp zotero.desktop ~/.local/share/applications/zotero.desktop
# You may need to modify zotero.desktop in your case
# You also can lanuch zotero by ./~/bin/zotero/zotero for test and debug
# From error I got, I should install libxt6 and for firefox
sudo apt install libxt6 libstartup

According to instructions on zotero forum, I change default port to avoid crostini crash. But I don’t forward port 23119 to 8090, I change both zotero and zotero connector port to 8090. It seems that zotero connector’ proxy redirection may cause connection lost, you can turn it off if you are in trouble.

In zotero: Edit -> Preference -> Advanced -> Config Editor -> Accept -> extension.zotero.httpServer.port -> double click and set to 8090

In zotero connector: Options -> Advanced -> Configuration -> Config Editor -> connector.url -> double click and set to http://127.0.0.1:8090/

It still be the issue for Poppler

END

Enjoy writing and programming on chromebook.

Begin at 2020/04/01 Final edit 2020/04/04

英文單詞記憶不濟的我，苦於 Chrome 上的拼寫檢查不穩定。可能在多語言環境下, chrome 沒 匹配對文本語言。後來我在谷歌網上應用搜到 Grammar and Spell Checker - LanguageTool，接着發現其服務本基於一個開源項目LanguageTool:

LanguageTool is an Open Source proofreading software for English, French, German, Polish, Russian, and more than 20 other languages. It finds many errors that a simple spell checker cannot detect… LanguageTool comes with its own embedded HTTP/HTTPS server so you can send a text to LanguageTool via HTTP and get the detected errors back as JSON.

在個人服務器上運行 LanguageTool，能提供免費版里缺失的功能，還能保護隱私。 同時社區提供了 Chrome, LibreOffice, Google Docs　對應的插件，應該也能找到 VIM，TexMacs 的插件。基本覆蓋了我書寫場景。 我沒有安裝 LanguageTool 到本地，而放在 VPS 的上。只要維護一個服務端，就能同時在 Chromebook, Fedora, Windows 上用。按照官方 Wiki 描述安裝:

1. 下載服務端程序

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wget https://languagetool.org/download/LanguageTool-stable.zip

2. 測試、運行服務端程序

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unzip LanguageTool*.zip
cd LanguageTool*
java -cp languagetool-server.jar org.languagetool.server.HTTPServer --port 8081 --allow-origin "*" --public

在本地測試服務端是否響應：

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curl --data "language=en-US&text=a simple test" http://your_server_ip:8081/v2/check

至此，已經實現 LanguageTool 基本功能。但用 Systemd 管理和添加 ngram 能讓它更省心、好用。

An n-gram is a contiguous sequence of n items from a text, like a girl (2-gram) or a tall girl (3-gram). Once you have a large amount of these n-grams with their number of occurrences, you can use this to detect errors in texts.

從官網下載 ngram-data, 解壓到某文件夾/.../ngrams，再添加參數 --languageModel "/.../ngrams" 指定 ngrams 所在文件夾啓動即可。

3. 用 Systemd 管理、維護

總不能一開開着 ssh 窗口運行命令，最好就用 Systemd. 新建 /usr/lib/systemd/system/lt.service.(Tested on Debian 10)

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[Unit]
Description=LanguageTool Service
After=network.target

[Service]
Type=simple
User=user_name # recomend non-root user
Restart=on-failure
RestartSec=5s
WorkingDirectory=/home/user_name/LanguageTool-4.8
ExecStart=java -Xmx1000M -cp /home/hf/LanguageTool-4.8/languagetool-server.jar org.languagetool.server.HTTPServer  --port 8081 --public --allow-origin "*" --languageModel "/home/hf/ngrams"
# -Xmx1000M is used to limit memory 1000M

[Install]
WantedBy=multi-user.target

啓動,並設開機啓動。

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systemctl enable lt.service
systemctl start lt.service

4. 插件使用

現在只試了 Chrome 和 Google Docs 插件。只需在插件設置里選擇、填寫服務端地址和端口。 接下來會試着用在 VIM, Texmacs 上，再改用 https 通信。

Kindle 有电子墨水屏和特有沉浸氛围，高中毕业的暑假，我买了第一个 Kindle(499)。我用 Kindle 看 RSS、课堂笔记、诗集。Kindle 的邮件传送服务能方便地传送文档到 Kindle, 只要 将文件以附件发邮件到指定邮箱就可。后来我又入手了 Sony 电纸书(DPT-RP1)。 DPT-RP1 用来 看文献，书最好。

用 KindleEar 推送 RSS 到 Kindle

这是一个运行在 Google App Engine(GAE) 上的 Kindle 个人推送服务应用，生成排版精美的杂志模 式mobi/epub格式自动每天推送至您的Kindle或其他邮箱。

我喜欢看博客，雖當下受众不廣，但喜欢它的独立、开放、不聒噪。訂閱每個博客的 RSS 後， 就成了一份只爲自己發行的報紙，而 Kindle 無疑是比液晶显示屏更舒服的载体。定期自動發 送到 Kindle 上，這更像一份報紙了。缺點就是和真的報紙一樣——看不了動圖和視頻，而且 這還是一份黑白報紙。

我用 cdhigh 开发的 KindleEar, 實現订阅 RSS , 定期发送到 Kindle. 按照官方 README 申请 GAE 之后，我通过 Google 云端 Shell 部署服务, 而不是官方 README 上用 Windows 腳本 (因主力不在 Windows)。 Bookfere 写好了一個自动部署脚本 KindleEar-Uploader：

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rm -f uploader.sh* && \
wget https://raw.githubusercontent.com/bookfere/KindleEar-Uploader/master/uploader.sh && \
chmod +x uploader.sh && \
./uploader.shh

另外我發現可以直接用這個腳本更新 KindleEar, 原有設置依然保留。

中文字体优化

一開始並不怎麼懂字體，只覺得可能會很更好看、舒服，就查查，折腾。但最後調出來的， 還不一定比自帶的字體好。值得一說的是，知道了一些關於字體的說法和知識。

和拉丁文字不同，中文印刷品幾乎不用斜體和粗斜體。中文的方塊字變斜體，就失去了方塊 字的特點。中文字體一般只需要常規體 (regular) 和粗體 (blod) 就可以了。

据研究，正文字型采用衬线字体 (Serif)（意思是在字的笔画开始、结束的地方有额外的装 饰，而且笔画的粗细会有所不同）如宋体可以提高阅读速度， 减少眼睛疲劳。 因此绝大多 数中文书籍都采用宋体作为正文字体。英文书籍也是一样采用衬线字体如 Times New Roman 等 作为正文字体。日语书籍采用的衬线体则一般是明朝体（Mincho，其实是宋体的别称）。
—- Kindle 中文字体替换”完美”方案探讨

印刷制品更多趋向使用衬线字体以方便阅读，但是在计算机领域中倾向使用无衬线字体 (國內稱黑體)以 方便在显示器上显示。此外，衬线字体从审美角度较为正式优美，然从眼睛的感受并不及 不采用衬线的黑体字，因为衬线体在笔划上有过多的点缀（笔划末端的小三角）很容易造 成视觉疲劳（尤其是显示在萤幕上时）。出于上述原因，大部分网页使用无衬线字体。 —- Wikipedia 襯線體

個人覺得Adobe 和 Google 合作的思源黑體和思源宋體是最普適、好看的開源中文字體。

不过，正如谷歌给思源系列起的名字「Noto」（No Tofu，消灭豆腐块）所示，思源字体开发 的主要目标在于提供一个尽可能覆盖汉字圈用字需求、减少无字可用现象的解决方案。 因此，尽管在设计上已经非常优秀，但思源系列并不是十全十美的。例如，不少专业从业人 员就指出思源黑体在笔画处理、行高等方面存在瑕疵；而思源宋体所附带的西文是没有斜体 的。当然，对于一款开源字体，我们似乎也不应过分苛求。

思源系列之外，虽然也存在一些中文开源字体，但往往在质量或字符集完整性上就较为逊 色了。文泉驿系列可能是一个较为可靠的选择，但在设计上并无太多可圈可点之处。 —- 免费字体获取和使用指南

中文字體產商有，方正、漢儀等。

用命令行发送文档

邏輯很簡單：配置好系统的邮件系统，讓它發送郵件到 Kindle. 最後写一个脚本，以文档 名为传入参数。可參考之前的博文。

最後更新於 2020/03/03

At this point, cognition science are the set of neuroscience, psychology, philosophy, linguistics, artificial intelligence, anthropology.

What are the past, now and future of cognition science?

We need to merge knowledge from different subjects.

As a life, life is so different comparing its environment. As a mind, mind is so different comparing its physical structure. How mind emerge(脱颖而出) from life?

Ref

1. Discussion on Zhihu

Last Update: Nov-2-2019

阳光原是穿过玻璃窗，射入办公室，但总是被帘子挡住。在 夏天，室外有着强烈的阳光。而室内，关着窗开着空调，让 我觉得这是一个防空洞。是我个人偏好的挑剔，但我还是不 禁想：这么美好的阳光，怎么能舍弃呢？那几支日光灯管怎 么能与“日月同辉”？古人看书喜欢几净窗明。古人在纸张、 布帛和竹简上阅读和书写，而我们阅读电子屏幕。前者正是 借助阳光实现与人的交流，但现在的电子屏幕却被反光困扰 着。我想如果出现了在阳光下不会反光的彩色电子屏，会不 不会改变。

知觉迟钝。说不上，是不是，大家对光线已经不敏感了。更 好用于思考的例子是大家对于声音的反应。可能和经历有关。

如果演奏之处，有明显的生活噪声，但在场者却没留意到。 那是真的吗？

更新：2019-10-19

The universe is an asymmetrical entity. I am inclined to believe that life as it is manifested to us must be a function of the asymmetry of the consequence of this fact. The universe is asymmetrical; for if one placed the entire set of bodies that compose the solar system, each moving in its own way, before a mirror, the image shown would not be superimposable on the reality. —- Louis Pasteur

In generally, I believe that universe is uniform at the first time of big bang. However, something subtle break uniformity. Then, snow ball became bigger and bigger. Finally, asymmetry creates what we are and where we live now. Based on energy conversation principle, although entity is symmetry, local is asymmetry. In other side, thermodynamics’ second law suggests that information which is the Maxwell demon, are able to break symmetry of system. So, what kind of mechanics break symmetry? What is the key point? How do the information be encode?(Hawking show similar idea in moive Into the Universe with Stephen Hawking)

Not just the huge universe, many thing do same. It is difficult and trickily to deal with the evolution of universe, to simplify question and have more fun, I would like to collect some cases around to find related threads and other interesting thing.

In the formation of moon, someone proposal that a much more weight part escape form Earth’s gravity by rotation. Then more and more dust were attracted by the first dust. Finally, Moon is as big as we know, which form a new balance. More interesting, Moon always face Earth on whole orbit. It must be something tricks occurs at some point.

In the study of cell migration, Prof. Huang found that two cell population which vary in moving speed cultured in same dish, are more easily to form cluster than cell which are same speed. Aha, whether are these similar with galaxy formation?

These “macro” pattern comes from simple and clear “micro” interaction. It is so amazing to know and find the structure of structure.

There fore it is impossible to have non-local conservation of charge. —- CPL,TCP

Nature uses only the longest threads to weave her patterns, so each small piece of her fabric revleas the organization of the entire tapestry. —- CPL,LG

Thre are also some very remarkable things, which are the near-symmetries. For instance, the remarkable feature of the fact that we can distinguish right and left is that we can only do so with a very weak effect, with this beta-disintegration. What this means is that nature is 99.99 per cent indistinguishable right from left, but that there is just one little piece, one little characteristic phenomenon, which is completely different, in the sense that that it is abosolutely lop-sided. This is a mystrey that no one has the slightest idea about yet. —- CPL, SPL

fluctuation, hierarchical structure

Reference:

[1]. 因为遗忘，麦克斯韦妖不可能存在 [2].

Last Update: Feb-27-2020

学校慧园 1 栋棵我觉得很神奇的小叶榄仁：全树原本为白色，但其中 一整枝却为翠绿色。更为有意思是，某次这棵树被台风吹倒后，我在绿 色的那一枝上发现了一个鸟窝。不经会思考这其中关联。同时我也在 行政楼前草坪上的小叶榄仁发现这个现象。我好奇这能怎么解释？

Question

Similar phenomenon also occur in other process, such as friction change during static object begin to move.

During phase transition, in order to overcome the critical point in certain direction, more energy or larger value should be used.

相变,滞后,暫態過程

Claim

Maxwell Reconostruction

Discussion

Reference

Abstract

A introduction and summary of dirac delta function and unit impulse function

Introdution

Histroy, usage, application

Detail

How to get the dirac delta function and unit impulse function? How the parameters drive these function evolution?

Phenomenon

In Drosophila, the ration of X chromosomes and autosomes determine the gender. When the ration larger than 1, we call it female; when ratio smaller than 0.5, we call it male; otherwise, we call it intersex.

What is the features of these gender?

Combination between Turing Pattern

Reference

More is difference. What is the mathematical shape?

Collections

Rule of The Large Number

To describe equilibrium properties of macroscopic bodies, stastical mechanics has to deal with very large number $N$ of microscopic freem degrees. Actually, taking the thermodynamic limit of $N\to\infty$ leads to a number of simplifications, some of which are describe in three types:

• Intensive quantities, such as temperature T, generalized forces.
• Extensive quantities, such as energy E, entropy S, and generalized displacements.
• Exponential dependence, that is $O(exp(N \phi))$, is encountered in enumerating discrete micro-states, or computing volumes in phase space.

In statistical mechanics, two simplify are used: summation of exponential quantities and saddle point integration.

When $N\to\infty$,

• 正则系统中一个假设:一个系统随时间演化称为是对时间的平均，其与多个 copy 的平均（也就是对系统的平均）是等价的。
• 极大似然
• Relationship between the genetics map distance and frequency. The genetics map distance always less than 50%. When genes number is large, the cross over is happen less.

The MPD

Ensemble Theory: Assuming a distribution of many copies of the same system(ensemble) in accessible phase space(deterimined by the connection between the system with the environments). The macroscopic properities of the system is just the average values of such ensemble. Different macroscopic environmental constrains different types of ensemble:

吉布斯现象

Reading: More is difference. Anderson

According to the quantunm description of microworld, the time and space are discret, while Manhattan distance may represente it. However, I found that we measure the world in continue method, such as Euclidean distance! In other wolds, the ruler has infinite accuracy. I confused in the measurement in time and space mostly. Another problem is how we align a ruler to objective. Detailing, how to find the objective edge in the view of ruler? Now and in the fucture, I wonder how we produce a measurement and how the discret distance(Manhattan Distance) transform to continue distance(Euclidean).

Idea

Because books can be sent to kindle by e-mail, linux shell scipts can do it well by a light mail system, such as neomutt with postfix. (Same idea should work in Mac and Windows with other packages At the end, we can send a book with a command easily. More, we can compile markdown notes to mobi file amd sent to kindle. Following are one of procedure.

Set Mail System

We use neomutt(or others) as a mail agent to organize mail, which generate mail and the command to send mail. Then postfix is used to sent mail to kindle mailbox, which excute command to send mail. Following is the introdution from their homepage:

NeoMutt is a command line mail reader (or MUA). It’s a fork of Mutt with added features

What is Postfix? It is Wietse Venema’s mail server that started life at IBM research as an alternative to the widely-used Sendmail program. Now at Google, Wietse continues to support postfix

Install neomutt and postfix:

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sudo pacman -S neomutt postfix

Then new a user config at ~/(or others). It is useful to set from option to a mail adresse which has enrolled under your kindle account. Meanwhile, this option can avoid our mail to be treated as junk:

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.neomuttrc
-------------------------------
set realname="H.F."
set from="moyuejian@outlook.com"

I following the predure in ArchLinux wiki to set up postfix. We need to uncommit the following line in /etc/postfix/aliases, and change you to a real user name:

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root: you

Once we have finished editing /etc/postfix/aliases we must run the postalias command and start/enable service:

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postfix /etc/postfix/aliases
sudo systemctl enable postfix.service
sudo systemctl start postfix.service

Test mail system and Send books to kindle

Now mail environment are done. We can test it:

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neomutt -s "Kindle mail env test" addressee

If you receive this mail, you can send a pdf file as attachment to kindle:

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neomutt -s "Sent book to kindle" kindle_addresse -a book.pdf

It maybe slow, you should wait or change other addressee. According to neomutt guide, -s means subject and -a means attachments(can be multi).

Just for convenience, I write a shell script:

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send_to_kindle.sh
---------------------------
#!/bin/bash
# Script to send books to kindle
# Usage  : kindle book1 book2
# Version: 0.2 (20181005 by H.F.)
if [ $# -eq 0 ] ; then                                               
  echo "Usage: kindle book1 book2 ...
  exit 1
fi
nowtime="`date +%Y-%m-%d`"
echo $* | neomutt -s "$*""$nowtime"  your_account@kindle.cn -a $*
echo "sent $* done :)"

And alias it to .bashrc(or others):

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echo "alias kindle='/path/send_to_kindle.sh'" >> .bashrc
source ~/.bashrc

Finally, books can be sent with single command:

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kindle book1 book1

Trouble Shooting

Some day I failed to send and get error:

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postdrop: warning: uid=1000: File too large
sendmail: fatal: hf(1000): message file too big

Following command enlarge the size limit to 2G:

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sudo postconf -e "message_size_limit=2048000000"
sudo postconf -e "mailbox_size_limit=2048000000"

Compile and Set Marddown notes to kindle

I always note in markdown when I take Cell Biology class, Genetics class etc. I want to review my note in kindle, so I write a scipt to do it. Markdown note compile to epub format by pandoc, then convert to mobi format by kindlegen.

KindleGen is a command line tool which enables publishers to work in an automated environment with a variety of source content including HTML, XHTML or EPUB. KindleGen converts this source content to a single file which supports both KF8 and Mobi formats enabling publishers to create great-looking books that work on all Kindle devices and apps.

Install pandoc and kindlegen(I find it in AUR)

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sudo pacman -S pandoc
yay kindlegen

Most of script are modifed from pandoc wiki(It is very useful). Following script is just a simple but workable example, you can modfiy it to generate a elegant e-book refer pandoc wiki.

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makebook.sh
---------------------------------------------------------
#!/bin/bash
# Desciption: Compile markdown note and sent to kindle
# Useage: ./makebook.sh
# Version: 0.2 20181005

## Book info
bookname="Cell Biology"
author="Yuejian Mo(collete)"

## add pandoc tag
echo "%"$bookname > title.txt
echo "%"$author >> title.txt

## markdown to epub, add chapter note here manually
pandoc -o CellBiology.epub title.txt \
README.md \
1.Introduction.md \
2.VisualizingCells.md
echo "Markdown to epub done"
rm title.txt

## epub ==> mobi
kindlegen CellBiology.epub > /dev/null # just hide show log
rm CellBiology.epub
echo "Epub to mobi done"

## send book to kindle mailbox
neomutt -s "$bookname"  your_account@kindle.cn -a CellBiology.mobi
echo "Sent done : )"

Todo: Try to write an CSS file to create better format for pandoc.

References

• Postfix homepage
• Neomutt
• Postfix configure in ArchLinux Wiki
• KindleGen homepage
• Pandoc Wiki

Final Aim: a script to transform PDB to .stl file

Last update: 08-15-2019

Reference

• https://pymolwiki.org/index.php/Blender
• https://openwetware.org/wiki/UCSF_Chimera_for_3D_Printing

小男孩，在水中欢乐地嬉戏。回到岸边，他问道：“师傅，溪水为什么这样 流？”师傅沉默地注视他片刻，回答说：“是土地让溪水这么流。”在返回寺庙的路上， 他们经过一座摇摇晃晃的小桥，小徒弟紧紧抓住师傅的手，望着脚下深深的水面， 问道：“师傅，峡谷为什么这么深？”在安全地到达对岸后，师傅回答他：“是溪水让 土地这么走” —- 《连接组》承现峻

宇宙越是显得被理解了， 就越显得没有意义。—-《最初三分钟》Steven Weinberg

我见那宇宙中环绕的令人战栗的空间，而我被囚系自这广袤中的一个角落，我不知 道我为何被放在这里而非别处，也不知道这赋予我生命的瞬间，为何是这时，而非 我之前和之后的永恒中的另一点。我环顾四周，只见无限，我在其中，就像一个原子， 又像一片影子稍纵即逝，后会无期。我唯一知道的，是我一定会死去，而我最不知道 的，恰恰就是这无法逃避的死亡。 —-《思想录》Blaise Pascal

警察遇到了一个趴在路灯下面的醉汉，那个醉汉解释说：“我的钥匙丢在墙角了。” 警察问的他：“那你为什么不去墙角找？”醉汉回答：“我看不见啊，现在只有路灯 下面有亮光啊” —- 《连接组》承现峻

在线虫的帮助下，愿我们足够努力和幸运，能有让人会心的发现 —- 江心庐

How to choose the method to lineage trace

Reference

• https://mp.weixin.qq.com/s?__biz=MzI5MDQzNjY2OA==&mid=2247489808&idx=1&sn=54e3595460df97a26a29a8617f963d78&chksm=ec1eba43db693355b7968a3cf7de15c6f70770248b8e175b21de04464396c21c0e88b6439ba2&mpshare=1&scene=23&srcid=1013DrvFkZCfU14rfScgonX3#rd

• The defination of random variable under some special frame. Ref to Bayesian logical Data Analysis for the Physical Sciences and book of Lyne.
• The relation between physical elements and statistical elements
• How to understand the operation of r.v. ? And how it map to real world? The operation of r.v. maybe the coordation transform.

Why we use random variable and sample space?

Box dimension can measure the set in a way that ingores irregularities of size less than $\epsilon$. It covering the set with boes os size $\epsilon$.

For we have in reality supposed that we can divide the phenomenon into two parts, one in which the discontinuity of the events taking place is essential while in the other it is trivial and ca be ignored.

Last update: 2020/07/17

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sudo pacman -S autossh
sudo useradd -m autossh
su -autossh
ssh-keygen
ssh-copy-id user@server.site

sudo vim /lib/systemd/system/autossh.service
[Unit]
Description=Auto SSH Tunnel
After=network-online.target
[Service]
User=autossh
Type=simple
ExecStart=/bin/autossh -p 22 -M 6777 -NR '*:6766:localhost:22' usera@site
ExecReload=/bin/kill -HUP $MAINPID
KillMode=process
Restart=always
[Install]
WantedBy=multi-user.targetq
WantedBy=graphical.target

sudo systemctl enable NetworkManager-wait-online
sudo systemctl enable autossh
sudo systemctl start autossh

It need to add hit key before start server

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ssh -p 6766 user@service.site

20180616: Meet the problem to start the script

Reference:

http://arondight.me/2016/02/17/%E4%BD%BF%E7%94%A8SSH%E5%8F%8D%E5%90%91%E9%9A%A7%E9%81%93%E8%BF%9B%E8%A1%8C%E5%86%85%E7%BD%91%E7%A9%BF%E9%80%8F/

QE

You are beautiful. Although your news down me, you are far away me.

It is far away to meet you. But I don’t down myself. Because the existence of youself, which has made sence and cliam me down. More, we have met and kown each other in MilchstraBe

I call it “congnitve triangulation,” and it is even more effective than numerical triangulation. It is based on the fact that when we encounter an unknown phenomenon, we try to connect it with thing that we already known.

However, if we can come up with a completely independent line of reasoning that gives us the same answer, we immediately take notice. Our brains cement our conclusions with an “aha!” moment, accompanied by feelings of joy and certainty—no doubt because two independent lines of thought arriving at the same conclusion are much likely to be caused by some regularity of the world than by sheet coincidence.

“A real electron and a real photon are maybe just fluctuations of the string-net”, Wen said. For example, water freezes into ice, by describing it as the breaking of a symmetry: Whereas liquid water hasrotational symmetry at the atomic scale (it looks the same in every direction), the $H_2O$ molecules in ice are locked in crystalline rows and colummns.

Things changed in 1982 with the discovery of phase called fractional quantum Hall states in an ultracold, two-dimensional gas of electrons.

In 1989, Wen imagined phases like the fractional quantum Hall states arising not on a plane, but on different toplogical manifolds—-connetcted spaces such as the surface of a sphere or a torus.

Researchers studying the genetic the genetic code have gradually determined that is codon-amino acid assignments are decidedly not random. They instead seem to be a product of natural selection, optimized to generate a favorable degree of genetic diversity, as well as to help safeguard the organism’s cells against the kinds of errors that tend to occur most frequently during the process of protein synthesis.

“For what we have.” said Chang Liu, a synthetic biologist at the University of California, Irvine, “it’s better than a one-in-a-million code.”

But while “the genetic code is a very long way from random,” Freeland said, “it’s also a very long way from perfect.” That is, it may be locally optimal—- the best of the many, many codes made possible by the chemistry of 20 amino acids —- but that doesn’t necessarily mean it’s globally best. “What Darwinism does.” Benner said, “is to search locally in the sequence space. You get by with what works.”

背景和要求

原先学校细胞房里控制流式细胞仪的电脑为了避免网络上的病毒等 影响，只好断开网线。流式细胞仪数据多是烧录到 CD/DVD。为了 方便，我们设法利用校园网和 Windows 系统自带的“网络驱动器”功能， 让用户可以在校园里随时随地下载实验数据到本地。同时利用 Windows 自带的防火墙限制系统只能访问内网资源。

方法

主要参考[1]. 首先设置所有的网络访问都被禁用。因为系统防火墙里 有很多的 Inbound and Outbound of Profile, 所以用 GitHub 上 的脚本 AdvFirewall Scripts 来限制所有的的进站和出站设置。下载源代码有，在源代码文件夹下 打开终端(按下 Shift, 再从右键菜单中打开)执行:

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install.cmd #　设置程序
netsh advfirewall set privateprofile firewallpolicy blockinbound,blockoutbound 
#限制所有的进站和出站

接着添加局域网段的 IP 范围到进站规则和出站规则。在开始菜单里搜 Windows Firewall with Advanced Security. 在 Inbound Rules 里单 击 New Rules, 选择 Custom Rule Type, 对所有程序和协议作用。 在 Scope 里允许所有 local IP addresses, 在 remote IP addresses 里填入 局域网网段范围。按默认选项往下走，最后保存。同样在 Ｏutbound Rules 里新建与 Inbound Rules 一样的规则。实验室计算机当前可访问 Inbound Rules 里的规则许可的 IP　对应的资源，例如 Form 系统。相对应的，符合 Outbound Rules 的实验室外计算机能够访问实验室计算机，同时也保证流式细胞仪能 也与实验室计算机通过 192.160.x.x 正常通信。

设置好　Outbound Rules 和 Inbound Rules 后，就可以设置共享文件夹了。 这步较为容易，可以在参考网上的示例。简单说，就是在文件夹的属性菜单 里共享，在高级共享里设置共享的名称和权限。记录下该实验室计算机 IP 和共享设置里的名称。在实验室外计算机，在文件游览器里填入类似 于 //IP//名称的服务器地址，再输入用户名和密码就能正常访问了。

进一步

和信息中心协助，搭实验数据远程平台。So Cytometer’s computer can be powered off.

参考

[1]. How can I restrict windows 7 to only use the local subnet, but block the internet

[2].https://en.wikipedia.org/wiki/IP_address [2]. http://www.techsupportforum.com/forums/f31/solved-how-to-disable-internet-connection-without-disabling-the-lan-network-232894.html

Because of limit free sync space of Zotero, I want to set a WebDAV server in my Aliyun server. WebDAV (Web-based Distrubuted Authoring and Versioning) bases on HTTP/1.1, which enables applications to read and write files in web server, even control versions. Both Apache and Nginx can hold WebDAV. Since Nginx has been install in my Aliyun server for Hexo, I only test on Nginx.

Although Nginx support the WebDAV, I still compile Nginx with nginx-dav-ext-module as ref 1. (I don’t confirm whether Nginx from apt-get has dav_ext_methods modules)

Here are two method. You can new a location below default http port(80)(ref 2), or new a server on other port(what I do). Nginx can check the configure file below /etc/nginx/sites-enabled, so following configure was created to a file.

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server {
	listen 9876; # port
	
	# set cilent body size to 1 G 
	client_max_body_size 1024M;
	location / {
		root /root/Zotero; # location of WebDAV in filesystem
		autoindex on;
		dav_methods PUT DELETE MKCOL COPY MOVE;
		dav_ext_mothods PROPFIND OPTIONS;
		create_full_put_path on;
		dav_access user:rw group:r all:r;
		auth_basic "Store for Zoter";
		auth_basic_user_file /etc/nginx/user.passwd;#password info
	}
}

Password info is created by

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htpsswd -c /etc/nginx/user.passwd hf

To avoid 413 error, you can type as following in configure file[ref 3]. client_max_body_size 1024M

Because I am using Aliyun server, I have to enable this port in the Aliyun control center.[ref] I don’t know what about other servers.

After restarting Nginx, you can open WebDAV as ip:9876 with username and password.

Reference

• 1. [编译Nginx]https://jameszhan.github.io/2015/02/25/setup-webdav-with-nginx-in-osx.html
• 1. Nginx 文件配置
• 1. 413 错误
• 1. 添加安全组规则

费歇尔曾把统计量(statistic)定义为：从观测值得出来的、可用来估计其分布参数的一个数值。

—- 第 9 章 钟形曲线

乌纳穆诺站起身来，从容地走向讲台，镇静地开始演讲：你们大家都记住我的话。你们都了解我，并且知道我 不可能保持沉默，因为沉默也可以解释为默认，沉默中常常意味着谎言。 实际上混沌理论是尝试着在一个更高端的层次上，通过复兴决定论(determinism)来动摇统计革命。 有写作者却总是用能力用非常简单而有说服力的方式表达复杂的思想，数学的发展在他们的表达中显得如此 的鲜明而平实。

—- 第 10 章 拟合优度检验

人们感觉到，他是那种有连续深度心智活动的人。

—- 第 14 章 数学界的莫扎特

我同意库恩的观点，我不相信人类的大脑能够构造一个理想的结构去解释、甚至不能近似地描述这个世界的 真实情况。……我们可以预计，统计革命最终将会走到它的终点，取而代之的是其它的什么东西。（但这个 过程令人兴奋，虽未能言传，小小的意会也令我心动）

应为统计革命的表面观念已经传播到现在文化中，越来越多的人相信所谓的真实性，而不考虑它的基本假设， 所以，让我们用统计的宇宙观来考虑下面三个哲学问题：

1. 可以用统计模型来做决策吗？
2. 当概率应用与现实生活中时其含义是什么？
3. 人们真的懂什么是概率吗？

—- 第 29 章 泥菩萨

Most avaible commit for Your Name.

版权归作者所有，任何形式转载请联系作者。

作者：余小岛（来自豆瓣）

来源：https://movie.douban.com/review/8086457/

日本和歌，歌词大意为：“梦里相逢人不见，若知是梦何须醒。纵然梦里常幽会，怎比真如见一回。”

一个人如果老是叫嚷着寂寞，多半是矫情。但一个人如果时常感到孤独，可能他真的就是孤独。寂寞是情随事迁的，孤独是自给自足的。寂寞是向外伸张索取的暗示，孤独是自成封闭回路的密码。寂寞会叫人闷得发慌，孤独却令人内心充实。

作为一个敏感、纤细、对孤独灵敏度很高的人，孤独和它的衍生物就可以把他的小世界修葺得苍翠繁盛。每一个脑洞都能幻化出波云诡谲、自成一体的宇宙。

更骄傲一点说，每个人的孤独只适合自己默读，怎么描述怎么体会怎么深入只有自己最清楚。 当一切摆在了台面，摆着与人沟通的姿态，反而失之完满。过于深入、局限地挖掘自己的小世界，有时会被诟病为赋新词强说愁，如果又没有一个着力点来支撑，难免显得小家子气。

https://movie.douban.com/review/8204951/

破裂的中心滤光片，梯度稀释。自然界设计的万物，从分子级别，到生态系统，总能发现这样令人

The Fourier transform(FT) decomposes a function of time (a signal) into the frequencies that make it up.

The Fourier transform of a funcition of time itself is a complex-valued function of frequency, whose absolute value represents the amount of that frequency present in the original function, and whose complex argument is the phase offset of the basic sinusoid in that frequency. The Fourier transform is called the frequency domain representation of the original signal.

Because we are talking about Fourier transoform, should we take about light in wave or partical?

Light in space-time

Light is part of electromagnetic wave, whose wavelength is about from 400nm-700nm and frequency range of roughly 430-750 THz. Electromagnetic wave refers to the waves(or their quanta, photons) of the electromagnetic field, propagation(radiating) through space-time, carring energy, momentum and angular momentum away from their source particle and can impart those quantities to matter with which they interact. Electromagnetic waves are synchronized oscillations of electric and magnetic fields that propagate at the speed of light through a vacuum.

(Why energy can be transport by oscillations of electric and magnetic field?)

Where light come from —- Light Source

• In energy
• In kinetics

Deceleration of a free charged particle, such as an electron, can produce visible radiation. (But Why electron’s energy choose to pass the energy into electric and magnetic field?) (How the energy of electron change to electromagnetic field?) (How the behavir of electron determin the frequency of light?)

Electron’s energy pass to electric and magnetic field.

How light transport?

The wavefront of electromagnetic waves emitted from a point source is a sphere.

It is different after emitting from source: the Near and far fields.

After emssion, for point light source, light is in planar wave. For paraell light, how different light transport together?

How to explain light with Fouier tranform?

The function of len and the mean of image

Light is measured with two main alternative sets of units: radiometry consists of measurements of light power at all wavelengths, while photometry measures light with wavelength weighted with respect to a standardised model of human brightness perception.

The len can do Fouier transform and inverse Fouier transform while the light throught it. The first len will transform space domain to frequency domain, then second len can transform information of frequency domain to space domain, which means object image will be recovered. If you want, you can modify the frequency domain information at the focus distance after the first len.

image plane.

How light is received?

Sense of light and Image of light. I wonder how to quantify the light of object.

Sound in space and time dimension

How human and sensor sence the light and sound?

以声音和图形来理解傅里叶解析.我们听到的声音究竟是什么，而麦克风听到的又是 什么？声音也是穷级数的物理图像吗？

参考

• https://www.zhihu.com/question/19714540
• Wikipedia: Electromagnetic radiation

Reference:

http://www.techmind.org/colour/index.html https://zh.wikipedia.org/wiki/%E8%89%B2%E6%B8%A9

Test

我天性不宜交际。在多数场合，我不是觉得对方乏味，就是害怕对方觉得我乏味。 可是我既不愿忍受对方的乏味，也不愿费劲使自己显得有趣，那都太累了。我独处时最 轻松，因为我不觉得自己乏味，即使乏味，也自己承受，不累及他人，无需感到不安。 —— 周国平 《风中的纸屑

来日可期.

在这个光怪陆离的人间，没有谁可以将日子过得行云流水。但我始终相信，走过平湖烟雨 ，岁月山河，那些历尽劫数、尝遍百味的人，会更加生动而干净。时间永远是旁 观者，所有的过程和结果，都需要我们自己承担——张爱玲

无限的梦，需要多少的努力和运气。

时而……，时而……

既是……，又是……

既是……，又是……，并时而……

如何怀揣不安,同时努力尝试。 —- Tari tari

Nice which is not same as beautiful, is a feeling that make other feel conforable.

• 能够单身，承受寂寞与难受。却不能把爱就此冷藏，也不要觉得自己的爱无人能接受。
• 思无邪，把爱变成礼物，而不是伤害。

• 我们知道的还是太少了
• 怎么？你被自己的不足吓哭了？把自己对无知的恐怖变成对朋友的气话？
• 如果担心失去而不去追，那最后的失去也在意料之中。

分吹落枯叶，枯叶滋养土壤，肥沃的土地帮助果实，缓慢而坚定地生长 —-<人生果实>

共振 非线性现象 Coupled Oscillators 素材：

• https://www.e-pit.jp/careerlab/2/1101
• http://www.hisenkei.net/ja/2012/index.html
• Travelling cortical waves

我来了，我累了，我好了，我走了

爱的深，一点也不错

你得不到，是因为不属于你；放不下，因为你不甘心

十年，可能太长，什么也可能改变；一生，可能太短，一件事也做不完

会议永远站是你身后 你不可以抛弃 可能拥抱

我依然怀念过去 可是不再留恋 因为我知道 有一日 我们都会在路的尽头再见

我是一个没明天的人 但我希望每个人都有明天

这个不是宿命，只是我的选择

世事如书 众生都有所爱那一句

I want to mark and present my thinking in refined and elegant, so Hexo become my choice now. The first post show how I set up web service in VPS and tune Hexo in own work flow.

Hexo is static blog framework. Hexo just is a manager to organize post and blog theme and complier( or generator) to compile Markdown documents to static html files mostly, which don’t host the web service as what WordPress doing.

So, Hexo is just installed and configured in my personal computer( Acer Chromebook). Firstly, I write post in Markdown using Vim. Then Hexo generate html from Markdown. Finally, copy these html files to blog server.

Setting Web and Sync Service in Remote

Nginx is used to host web service and Git is used to sync the html files which Hexo generate.

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# install Nginx and Git
apt install git nginx
# start Nginx service, default test page: http://server-ip
systemctl start nginx

For security, a non-root user should be used to operate html files in Nginx and Git.

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# add non-root user, called hf(or other)
adduser hf # or useradd hf

Then create special folder to store blog html files and configure Nginx

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# store blog html files in /var/www/blog/html/
mkdir -p /var/www/blog/html
# change the owner and perimission to above non-root user, so Git can to modify
chown -R $USER:$USER /var/www/blog/html  # Replace $USER to hf(or other you want)
chmod -R 755 /var/www/blog/html
touch /etc/nginx/conf.d/blog.conf
vim /etc/nginx/conf.d/blog.conf

Fill blog.conf as:

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server {
    listen 80;
    listen [::]:80; # for ipv6

    root /var/www/blog/html;
    index index.html index.htm index.nginx-debian.html;

    server_name blog.whitecrow.xyz

    location /{
        try_files $uri $uri/ =404;
        }
    }

Restart Nginx service to apply change

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systemctl restart nginx

Until now, once copy the html files into /var/www/blog/html, blog will work as expected. Copy from local to VPS manual all the time, is boring and cause mistake. I use git and hexo-deployer-git to auto sync html files once Hexo generate, which called deploy. In remote, I create a bare git repo only for sync html files.

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cd /home/hf # Anywhere you want
git init --bare blog.git # Any repo name you want

A git hooks post-receive can auto copy html files to target folder once git push operation finish. I new a post-receive in blog.git/hooks as

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#!/bin/sh
git --work-tree=/var/www/blog/html --git-dir=/home/hf/bolg.git checkout -f
# work-tree is where store html files, replace it for yourself

Next steps are done in local.

Install and Set Hexo in Local

In my way, Hexo is only installed in local, my chromebook. Some basic configurations are required to run Hexo correctly.

Install Hexo as official document

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# Install Node Version Manager nvm
wget -qO- https://raw.githubusercontent.com/nvm-sh/nvm/v0.34.0/install.sh | bash
# Install Node.js
nvm install stable 
# Install Hexo
npm install -g hexo-cli# add --registry=https://registry.npm.taobao.org in China
# Install Git
apt install git
# Install hexo-depolyer-git for auto deploy if you need
npm install hexo-deployer-git --save
# Install hexo server for local server if you need
npm install hexo-server --save
# add --registry=https://registry.npm.taobao.org in China

Initialize Hexo in the target <folder>, which isn’t required for migiration Hexo from exited project.

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hexo init <folder>
cd <folder>
npm install

After initialization or migration, I set up git deploy by modify <folder>/_config.yml. How does it work exactly, official document has nice explanation.

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deploy:
- type: git
  repo: hf@blog.whitecrow.xyz:blog
  branch: master
- type: git # This isn't required for normal work.
  repo: git@github.com:JiangXL/<repo name>
  branch: public # Because I want to back to GitHub by the way.

Although I use GitHub host Hexo project, deploying html files to my blog.git in remote don’t disorder each other. So, once order deploy command, push still be ordered in GitHub repo’s master branch.

Now you can skip to final section to begin the first post.

Tune Blog Theme in Hexo

Enable TeX support by MathJax, see this post Due to cross-talking between MathJax and Markdown, I change the render as

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npm uninstall hexo-renderer-marked
npm install hexo-renderer-kramed --save

Chinese/ English, Breaking, TeX format…

Todo:

• Remove the last/next post link at end of page.
• Simplify homepage

It is high time to enjoy writing

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cd <folder>
hexo new <post name>
# or use a draft layout, which don't render to html files
hexo new draft <post name>
vim <source_post/pos name>
# ...
# bla bla
# 
hexo g -d # depoly post to web server
git add . # Commit to GitHub, which isn't required for normal usage
git commit -a
git push

Before deploying, I always open a local Hexo server, which render html files, watch for file changes and update automatically.

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hexo s

Blog can be preview in local-ip:4000

Last update: 08-14-2019

Reference

• https://eliyar.biz/how_to_build_hexo_blog/
• http://www.swiftyper.com/2016/04/17/deploy-hexo-with-git-hook/
• https://hexo.io