# Complex data types and the Rust FFI

The Rust Foreign Function Interface (FFI, for short) is a feature of Rust that enables the sharing of data and functions between parts of code that have been written in different languages. I am interested in the FFI because many libraries used in embedded systems are written in C, and I would like to leverage them for my embedded work with Rust.

I quickly learned from my initial experiments with the Rust FFI that one of its challenges is casting data types into a form that may be consumed by other languages. This challenge is not unique to the Rust FFI, and there are numerous reasons for it. For one, different languages use different mechanisms to layout data in the computer's memory. What's more, names for functions and data types are often mangled, which means that the symbol in a library that maps to a function may be different than the name that you give to the function in your code. As far as I know, C compilers do not mangle symbol names, and partly for this reason the C language is often used as an intermediary language in FFIs. Converting Rust to C is therefore an important skill when using Rust for multi-language work.

There are a few good resources on the internet about using the Rust FFI to expose functions written in Rust to other languages. However, I found little information about passing data types between languages. To help remedy this situation, I describe in this post a simple Rust library that I wrote to explore how to pass complex data types from Rust to C.

## An example FFI project

I created the Rust library in the typical way by first starting a new project with Cargo:

$cargo new --lib rstruct$ cd rstruct


Inside, I modified the contents of Cargo.toml to the following:

[package]
name = "rstruct"
version = "0.1.0"
authors = ["Kyle M. Douglass"]
edition = "2018"

[lib]
crate-type = ["cdylib"]

[dependencies]


The only lines that I added were [lib] and crate-type = ["cdylib"]. As described in the 2018 edition guide, this type of crate produces a binary that has no Rust-specific information in it and is intended for use through a C FFI.

Next, I opened the src/lib.rs source file, removed the auto-generated content, and added the following source.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 use std::boxed::Box; use std::ffi::CString; use std::os::raw::c_char; #[repr(C)] pub struct RStruct { name: *const c_char, value: Value, } #[repr(C)] pub enum Value { _Int(i32), _Float(f64), } #[no_mangle] pub extern "C" fn data_new() -> *mut RStruct { println!("{}", "Inside data_new().".to_string()); Box::into_raw(Box::new(RStruct { name: CString::new("my_rstruct") .expect("Error: CString::new()") .into_raw(), value: Value::_Int(42), })) } #[no_mangle] pub extern "C" fn data_free(ptr: *mut RStruct) { if ptr.is_null() { return; } unsafe { Box::from_raw(ptr); } } 

Roughly speaking, this simple library does two things. First, it defines two data types, a struct called RStruct and a Rust enum (not to be confused with a C enum!) called Value. Second, it exposes two functions that may be used to access instances of these data types from C: data_new() and data_free().

Let's take closer look now at what the code is doing.

## Defining structs and enums for use in C

I want to expose instances of the RStruct type to C code. The definition of RStruct is

#[repr(C)]
pub struct RStruct {
name: *const c_char,
value: Value,
}


The first line here is [repr(C)]. This is an attribute that modifies the layout of the struct in memory to "do what C does." As described in the Rustonomicon,

The order, size, and alignment of fields is exactly what you would expect from C or C++. Any type you expect to pass through an FFI boundary should have repr(C), as C is the lingua-franca of the programming world.

Next, we define a public struct just as we would if we were writing typical Rust code. In this example, the struct has two fields. The first is a field called name, which has a type *const c_char. The Rust data types String and &str cannot be interpreted in C, so instead we define the data type as a raw pointer to a c_char. (In this case, * is not dereferencing the pointer but is part of the type name *const T.)

The second field is an enum whose definition follows:

#[repr(C)]
pub enum Value {
_Int(i32),
_Float(f64),
}


Again we use #[repr(C)] to indicate that we want the enum to be laid out in memory in the same manner as in C. The enum Value has two variants, _Int and _Float, that each contain a value of i32 and f64, respectively. If you're familiar with C, then you may have already noticed that C enums are differnt from Rust enums in that they do not hold any data themselves. How this minor annoyance is solved will be seen later when we generate the C header for this library.

The data types i32 and f64 are easily translated into C's equivalent numeric data types, so there is no need to do anything special with them.

### Instantiating and freeing Memory

Following the data type definitions, there are two functions that are exposed through the FFI boundary, one for instantiating an RStruct and one for freeing the memory associated with an RStruct. The method for instantiation is first:

#[no_mangle]
pub extern "C" fn data_new() -> *mut RStruct {
println!("{}", "Inside data_new().".to_string());

Box::into_raw(Box::new(RStruct {
name: CString::new("my_rstruct")
.expect("Error: CString::new()")
.into_raw(),
value: Value::_Int(42),
}))
}


The first line contains an attribute called #[no_mangle]. As defined in the Book:

Mangling is when a compiler changes the name we’ve given a function to a different name that contains more information for other parts of the compilation process to consume but is less human readable.

Placing the #[no_mangle] attribute before the function definition ensures that the function name matches that of the corresponding symbol in the library.

Next is the function definition pub extern "C" fn data_new() -> *mut RStruct. Let's break this down into parts to understand it better:

• pub : The function will be callable from outside the library
• extern "C" : This line serves two different purposes in Rust, both related to FFI. In my case, I use it specify that the function should be exposed with the application binary interface from C.
• fn data_new() : This is just the usual fn keyword and the name of the function
• -> *mut RStruct : Here I specify that the function will return a mutable, raw pointer to an RStruct instance.

The purpose of this function is to create a RStruct instance and return a pointer to it. The RStruct is created just as we would any other struct in Rust, with the exception of the name field:

RStruct {
name: CString::new("my_rstruct")
.expect("Error: CString::new()")
.into_raw(),
value: Value::_Int(42),
}


The CString is first created with the new() constructor and contains the value "my_rstruct". After unpacking the result with expect(), I call the into_raw() method to create a raw pointer to the C string whose ownership will be passed off to the calling C code. (If I had used as_ptr() instead, the pointer would have been dropped immediately after the function call because the CString would have been deallocated.) The value field is instantiated as it would be in normal Rust.

What is perhaps new in this method is the Box type that wraps the RStruct instance.

Box::into_raw(Box::new( ... ))


A Box is one of Rust's smart pointers that is used to allocate memory for a data type on the heap. When Box::new() is called it creates a pointer to the newly created RStruct instance. Normally, this pointer would be dropped and the memory automatically deallocated when the data_new() function returns. However, the Box::into_raw() function serves the same purpose here as the corresponding function for CString: it hands off ownership of the pointer to the calling code so that the memory is not deallocated.

There is a rule-of-thumb that memory allocated by Rust should be freed by Rust. For this reason, we provide the data_free() method that C code may use to deallocate the memory that is allocated by data_new().

#[no_mangle]
pub extern "C" fn data_free(ptr: *mut RStruct) {
if ptr.is_null() {
return;
}
unsafe {
Box::from_raw(ptr);
}
}


This function accepts a mutable pointer to an RStruct. First, it checks whether the pointer is null and if it is, the function returns without doing anything. Assuming that the pointer is not null, the Box is reconstructed from it inside an unsafe block because from_raw() is unsafe. Importantly, this new Box pointer will go out of scope at the end of the function so that it will automatically be dropped when the function returns.

Building the library is simple. I run cargo build --release to build a release version. The library itself will be found at target/release/librstruct.so. On Linux, one can verify that it contains the data_new() and data_free() methods by displaying its symbols with the nm -g command:

$nm -g target/release/librstruct.so # snip 00000000000046c0 T data_free 00000000000044e0 T data_new # snip  ### Generating the header for the library Now that I have a shared library, I want to access the functions that it exposes from C. To do this, I first need a header file that I can use to import the library's declarations into the C code. Moreover, generating the header can help in understanding how Rust translates its data types to C. I will use cbindgen to automatically generate the header. cbindgen is installed with the command $ cargo install cbindgen


cbindgen is highly configurable, but for the project described here I only need its most basic functionality. Assuming that I am in the root directory of my Rust project, I generate the header rstruct.h with the following

$cbindgen --lang C -o rstruct.h .  After running cbindgen there is a new file called rstruct.h in the project folder. Here are its contents:   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 #include #include #include #include typedef enum { _Int, _Float, } Value_Tag; typedef struct { int32_t _0; } _Int_Body; typedef struct { double _0; } _Float_Body; typedef struct { Value_Tag tag; union { _Int_Body _int; _Float_Body _float; }; } Value; typedef struct { const char *name; Value value; } RStruct; void data_free(RStruct *ptr); RStruct *data_new(void);  First, you can see the enum that contains the variations of the Value data type that is stored in the RStruct and that was defined in Rust. The name of this new type is Value_Tag, and it is used to define the current type of a value. typedef struct { Value_Tag tag; union { _Int_Body _int; _Float_Body _float; }; } Value;  A Value is just another struct that contains a Value_Tag field to identify which variant of the enum it is holding and a union field that holds the actual value. The important thing to understand here is that cbindgen effectively uses nested C data types to represent complex Rust data structures. In particular, Rust enums are a combination of C structs, enums, and unions. ## Calling the library from C With everything in place, it's now time to write the C program. My example C program looks like the following:   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 #include #include #include #include "rstruct.h" int main() { void* handle; RStruct* (*data_new)(void); void (*data_free)(RStruct*); char* error; printf("Loading librstruct.so...\n"); handle = dlopen( "librstruct.so", RTLD_LAZY ); if (!handle) { fprintf(stderr, "%s\n", dlerror()); exit(EXIT_FAILURE); } printf("Done.\n\n"); dlerror(); data_new = (RStruct* (*)(void)) dlsym(handle, "data_new"); error = dlerror(); if (error != NULL) { fprintf(stderr, "%s\n", error); exit(EXIT_FAILURE); } dlerror(); data_free = (void (*)(RStruct*)) dlsym(handle, "data_free"); error = dlerror(); if (error != NULL) { fprintf(stderr, "%s\n", error); exit(EXIT_FAILURE); } printf("Calling data_new() from main.c...\n"); RStruct* data = (*data_new)(); printf("\nBack inside main.c. Printing results...\n"); printf("Name: %s\nValue: %d\n", data->name, data->value._int._0); printf("\nFreeing the RStruct data...\n"); (*data_free)(data); dlclose(handle); return EXIT_SUCCESS; }  This code is based on the example in the dlopen() man pages. In particular, the library file is opened and a handle attached to it here: handle = dlopen( "librstruct.so", RTLD_LAZY );  A function pointer to data_new() is created with dlsym(), and we use the function to create the new RStruct instance with the lines data_new = (RStruct* (*)(void)) dlsym(handle, "data_new"); // snip RStruct* data = (*data_new)();  Finally, the data is freed by creating another function pointer to data_free() and calling it. data_free = (void (*)(RStruct*)) dlsym(handle, "data_free"); // snip (*data_free)(data);  ### Running the program I wrote a small Makefile to handle compilation of the C and Rust programs while I wrote this post. I won't include it here because it distracts from the main message about the Rust FFI. Instead, I will describe how to compile the program from the command line. I first placed the librstruct.so, rstruct.h, and main.c programs into the following directory structure: $ tree
.
├── include
│   └── rstruct.h
├── lib
│   └── librstruct.so
└── src
└── main.c


Next, I compiled the main binary with gcc.

$gcc -Wall -g -Iinclude -c -o main.o main.c$ gcc -Wall -g -o main main.o -ldl


(-ldl is used to link against libdl for dynamically loading the library from C.) After compilation I run the main binary. To make it work, I set the LD_LIBRARY_PATH environment variable so that the program knows to look inside the lib directory for the librstruct.so library.

$cd rust-uds  Next, I opened the file that cargo automatically generated in src/main.rs, removed the auto-generated content, and added the following code, which is largely based on the example provided in the Rust documentation but with a few key differences:   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 use std::io::{BufRead, BufReader}; use std::os::unix::net::{UnixStream,UnixListener}; use std::thread; fn handle_client(stream: UnixStream) { let stream = BufReader::new(stream); for line in stream.lines() { println!("{}", line.unwrap()); } } fn main() { let listener = UnixListener::bind("/tmp/rust-uds.sock").unwrap(); for stream in listener.incoming() { match stream { Ok(stream) => { thread::spawn(|| handle_client(stream)); } Err(err) => { println!("Error: {}", err); break; } } } }  ## Explanation The first three lines import the necessary modules for this code example. use std::io::{BufRead, BufReader}; use std::os::unix::net::{UnixStream,UnixListener}; use std::thread;  BufRead is a trait that enables extra ways of reading data sources; in this case, it has an internal buffer for reading the socket line-by-line. BufReader is a struct that actually implements the functionality in BufRead. UnixStream and UnixListener are structs that provide the functionality for handling the UNIX socket, and the std::thread module is used to spawn threads. The next set of lines defines a function named handle_client() that is called whenever new data arrives in the stream. The explanation for this is best left until after the main() function. The first line in the main() function creates the UnixListener struct and binds it to the listener variable. let listener = UnixListener::bind("/tmp/rust-uds.sock").unwrap();  The bind() function takes a string argument that is a path to the socket file and unwrap() moves the value out of the Result that is returned by bind(). (This is a pattern that is discouraged in Rust but is OK for quick prototypes because it simplifies the error handling.) After creating the listener, listener.incoming() returns an iterator over the incoming connections to the socket. The connections are looped over in an infinite for loop; I believe that this is more-or-less the same as a generator in Python which never raises a StopIteration exception. Next, the Result of the incoming streams is matched; if there is an error, it is printed and the loop it exited: Err(err) => { println!("Error: {}", err); break; }  However, if the Result of the connection is Ok, then a new thread is spawned to handle the new stream: Ok(stream) => { thread::spawn(|| handle_client(stream)); }  Finally, the client handler is called for each connection. fn handle_client(mut stream: UnixStream) { let stream = BufReader::new(stream); for line in stream.lines() { println!("{}", line.unwrap()); } }  The handler in this case is fairly straight-forward. It shadows the original stream variable by binding it to a version of itself that has been converted to a BufReader. Finally, it loops over the lines() iterator, which blocks until a new line appears in the stream. ## Sending messages As an example, let's send messages to the Rust program via Bash using the OpenBSD version of netcat. (The OpenBSD version seems to be the default on Ubuntu-based systems.) This should underscore the fact that the UNIX socket is really being used to communicate between two different processes. First, compile and run the Rust program to start the socket listener: $ cargo run --release
Compiling rust-uds v0.1.0 (/home/kmd/src/rust-uds)
Finished release [optimized] target(s) in 1.59s
Running target/release/rust-uds


Open up a new terminal. You should see the socket file /tmp/rust-uds.sock:

$ls /tmp | grep rust rust-uds.sock  Now let's send messages to the rust program. Use the following netcat command to open a connection to the socket. $ nc -U /tmp/rust-uds.sock


The -U is necessary to indicate to netcat that this is a UNIX stream socket. Now, start typing text into the same window. Every time you press ENTER, you should see the same text appear in the terminal window in which the Rust program is running. Press CTRL-C to exit the Rust socket listener. If you re-run the program, delete the old socket first: rm /tmp/rust-uds.sock

## Summary

• Use a UnixListener struct to create a UNIX socket and listen to it for connections.
• Print each new line in the stream by iterating over the lines() iterator of the BufReader.
• Send commands to your Rust program from bash with nc -U "$PATH_TO_SOCKET". # Linking shared libraries in Micro-Manager for Linux Lately I have been working on a new Video4Linux2 device adapter for Micro-Manager. I encountered the following error after adding some functionality that introduced two Boost libraries as new dependencies in my project. Traceback (most recent call last): File "RPiV4L2.py", line 17, in <module> mmc.loadDevice("camera", "RPiV4L2", "RPiV4L2") File "/home/micro-manager/app/lib/micro-manager/MMCorePy.py", line 3515, in loadDevice return _MMCorePy.CMMCore_loadDevice(self, label, moduleName, deviceName) MMCorePy.CMMError: Failed to load device "RPiV4L2" from adapter module "RPiV4L2" [ Failed to load device adapter "RPiV4L2" [ Failed to load module "/home/micro-manager/app/lib/micro-manager/libmmgr_dal_RPiV4L2.so.0" [ /home/micro-manager/app/lib/micro-manager/libmmgr_dal_RPiV4L2.so.0: undefined symbol: _ZN5boost10filesystem6detail13dir_itr_closeERPvS3_ ] ] ]  I received this error when I tried to load the device in a Python script. At first I was puzzled because the code compiled without problems, but I soon found that the solution was simple. The key part of the message is undefined symbol: _ZN5boost10filesystem6detail13dir_itr_closeERPvS3_. To troubleshoot this, I first demangled the symbol name by entering it at https://demangler.com/. I discovered that the symbol was referring to the function boost::filesystem::detail::dir_itr_close(void*&, void*&). I had added both the Boost filesystem and Boost regex libraries to this device adapter as dependencies, so it was not surprising that either of their names appeared in the error message. Next, I used the ldd program to check which libraries my device adapter were linked against. (libmmgr_dal_RPiV4l2.so.0 is the name of the device adapter library file). $ ldd libmmgr_dal_RPiV4L2.so.0
linux-vdso.so.1 (0x7ec21000)
libdl.so.2 => /lib/arm-linux-gnueabihf/libdl.so.2 (0x76e9c000)
libstdc++.so.6 => /usr/lib/arm-linux-gnueabihf/libstdc++.so.6 (0x76d54000)
libm.so.6 => /lib/arm-linux-gnueabihf/libm.so.6 (0x76cdc000)
libc.so.6 => /lib/arm-linux-gnueabihf/libc.so.6 (0x76bee000)
libgcc_s.so.1 => /lib/arm-linux-gnueabihf/libgcc_s.so.1 (0x76bc1000)
libicudata.so.57 => /usr/lib/arm-linux-gnueabihf/libicudata.so.57 (0x75334000)
libicui18n.so.57 => /usr/lib/arm-linux-gnueabihf/libicui18n.so.57 (0x75187000)
libicuuc.so.57 => /usr/lib/arm-linux-gnueabihf/libicuuc.so.57 (0x7505e000)
librt.so.1 => /lib/arm-linux-gnueabihf/librt.so.1 (0x75048000)
/lib/ld-linux-armhf.so.3 (0x76fb4000)


Neither libboost_filesystem nor libboost_regex are listed, so I knew that they were not linked with the device adapter.

There is a Makefile.am included in the directory of every device adapter in the Micro-Manager project. This file is used by Autotools define how the device adapter should be compiled and linked. Here is what my Makefile.am looked like:

 1 2 3 4 5 AM_CXXFLAGS = $(MMDEVAPI_CXXFLAGS) deviceadapter_LTLIBRARIES = libmmgr_dal_RPiV4L2.la libmmgr_dal_RPiV4L2_la_SOURCES = RPiV4L2.cpp RPiV4L2.h refactor.h ../../MMDevice/MMDevice.h ../../MMDevice/DeviceBase.h libmmgr_dal_RPiV4L2_la_LIBADD =$(MMDEVAPI_LIBADD) libmmgr_dal_RPiV4L2_la_LDFLAGS = $(MMDEVAPI_LDFLAGS)  After experimenting a bit, I discovered that I could instruct the linker to link against shared libraries by adding them to the libmmgr_dal_RPiV4L2_la_LDFLAGS variable with the -l flag. The resulting line now looks like: libmmgr_dal_RPiV4L2_la_LDFLAGS =$(MMDEVAPI_LDFLAGS) -lboost_regex -lboost_filesystem


Finally, running ldd on the rebuilt device adapter now shows these two libraries:

$ldd libmmgr_dal_RPiV4L2.so.0 linux-vdso.so.1 (0x7ed74000) libboost_regex.so.1.62.0 => /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.62.0 (0x76e3c000) libboost_filesystem.so.1.62.0 => /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.62.0 (0x76e1b000) ...  # Create a custom Raspbian image with pi-gen: part 2 In my previous post, I discussed how to setup user accounts and locales in a custom Raspbian image using pi-gen. In this follow-up post, I will discuss the main problems that I want to solve: automatically configuring the wireless network and ssh on a new Raspberry Pi without a terminal attached directly to the Pi. ## Set up the wireless network ### The WPA supplicant The Pi's wireless credentials are configured in stage 2 in the file stage2/02-net-tweaks/files/wpa_supplicant.conf. Here's how it looks by default: ctrl_interface=DIR=/var/run/wpa_supplicant GROUP=netdev update_config=1  According to the blogs Learn Think Solve Create and the Raspberry Spy, the first thing we should do is add our country code to the top of this file with the line country=CH. (Use your own country code for this.) Next, we want to enter the details for our wireless network, which includes its name and the password. For security reasons that I hope are obvious, we should not store the password in this file. Instead, we create a hash of the password and put that inside the file. The command to create the password hash is wpa_passphrase ESSID PASSWORD > psk  where ESSID is our wireless network's name. Note that I also used a space before the wpa_passphrase command to prevent the password being written to my .bash_history file. Now, we copy and paste the contents of the file psk into the wpa_supplicant.conf and remove the comment that contains the actual password: country=CH ctrl_interface=DIR=/var/run/wpa_supplicant GROUP=netdev update_config=1 network={ ssid=YOUR_ESSID_HERE psk=YOUR_PSK_HASH_HERE }  ### Configure the wireless network interfaces After having configured the supplicant, we next move on to configuring the network interfaces used by Raspbian. The appropriate file is found in stage1/02-net-tweaks/files/interfaces. In my post Connecting a Raspberry Pi to a Home Linux Network I described how to set up the network interfaces by editing /etc/network/interfaces. Much of the information presented in that post has now been superseded in Raspbian by the DHCP daemon. For now, we will use the interfaces file to instruct our Pi to use DHCP and will use /etc/dhcpcd.conf at a later time to set up a static IP address when provisioning the Pi. We first need to make a few changes to make the interfaces file aware of the credentials in the wpa supplicant configuration file. According to the blog kerneldriver, we need modify the /etc/networe/interfaces file as such: auto lo iface lo inet loopback iface eth0 inet dhcp auto wlan0 iface wlan0 inet manual wpa-roam /etc/wpa_supplicant/wpa_supplicant.conf iface default inet dhcp  In the first modification, I specify that I want the wirless interface wlan0 started automatically with auto wlan0. Next, I specify that the wlan0 interface should use the manual inet address family with the line iface wlan0 inet manual. According to the man pages, "[the manual] method may be used to define interfaces for which no configuration is done by default." After this we use the wpa-roam command to specify the location of the wpa_supplicant.conf file that we previously modified. The wireless ESSID and password are therefore not defined in interfaces, but rather reference them inside wpa_supplicant.conf. In case you noticed that wpa-roam doesn't appear as an option in documentation on the interfaces file and were wondering why, it's because other programs like wpasupplicant may provide additional options to the interfaces file. A similar command is wpa-conf, but I do not quite yet understand the difference between these two commands. Following the wpa-roam command, we configure the default options for all networks in our wpa_supplicant.conf file with the line iface default inet dhcp. At this point, we save the setup of the static IP address for a later time. For more information, see the interfaces man page for Debian Stretch. ### Change the hostname Our Pi's hostname may be changed from the default (raspberrypi) by modifying the line in stage1/02-net-tweaks/files/hostname. See RFC 1178 for tips on choosing a hostname. In addition to modifying the hostname file, we need to update stage1/02-net-tweaks/00-patches/01-hosts.diff and change raspberrypi to the new hostname: Index: jessie-stage1/rootfs/etc/hosts =================================================================== --- jessie-stage1.orig/rootfs/etc/hosts +++ jessie-stage1/rootfs/etc/hosts @@ -3,3 +3,4 @@ ff02::1 ip6-allnodes ff02::2 ip6-allrouters +127.0.1.1 NEW_HOSTNAME_HERE  ### Set the DNS servers DNS servers are configured in export-image/02-network/files/resolv.conf. By default, mine was already configured to use one of Google's DNS servers (8.8.8.8). I added a secondary Google DNS address as well: nameserver 8.8.8.8 nameserver 8.8.4.4  ## Enable SSH Enabling SSH is simple. Open stage2/01-sys-tweaks/01-run.sh and change the line systemctl disable ssh to systemctl enable ssh. (I later learned that we can also enable ssh on a headless pi by adding an empty file named ssh to the boot partition of a standard Raspbian image. See here for more details: https://www.raspberrypi.org/documentation/remote-access/ssh/) ### Configuring SSH keys (or not) I decided after writing much of this tutorial that pi-gen was not necessarily the best tool for adding my public SSH keys. So long as I have network access and SSH enabled, I can easily add my keys using ssh-copy-id. Furthermore, after following this tutorial, there still remains a lot of setup and customization steps. These can more easily be performed manually or by server automation tools like Fabric or Ansible. Therefore, I think that at this point we can stop with our customization of the image with pi-gen and move to a different tool. We have a basic Raspbian image that is already configured for our home network and that serves as a starting point for more complete customization. ## Conclusion This tutorial and my previous post demonstrated how to create a custom Raspbian image that is pre-configured for • our home wireless network • our locale information • ssh Of course, we can do much, much more with pi-gen, but other tools exist for the purpose of configuring a server. These tutorials at least allow you to setup a new Raspberry Pi without having to manually configure its most basic functionality. Happy Pi'ing! # Create a custom Raspbian image with pi-gen: part 1 Docker has been an amazing tool for improving my development efficiency on the Raspberry Pi. For example, I recently used it to cross-compile a large C++ and Python library for the Pi's ARM architecture on my x86_64 laptop. However, in that post I took it for granted that I had already set up my Raspberry Pi with user accounts, packages, ssh keys, etc. Performing these steps manually on a fresh install of the Pi's Raspbian operating system can become tedious, especially because ssh needs to be manually enabled before doing any remote work. Fortunately, the Raspberry Pi developers have provided us with pi-gen, a useful collection of Shell scripts and a Docker container for creating custom Raspbian images. In this post, I will summarize the steps that I take in using pi-gen to create my own, personalized Raspbian image. After I wrote this post, I found a set of posts at Learn Think Solve Create that describe many of the tasks I explain here. Be sure to check them out for another take on modifying Raspbian images. ## Clone the pi-gen repository This is as easy as cloning the git repository. git clone git@github.com:RPi-Distro/pi-gen.git  Alternatively, you can use the https address instead of ssh, which is https://github.com/RPi-Distro/pi-gen.git. From now on, all directories in this post will be relative to the root pi-gen directory. ## Build the official Raspbian images By default, the pi-gen repository will build the official Raspbian images. Doing this once before making any modifications is probably a good idea; if you can't build the official images, how will you be able to build a custom image? There are two main scripts that you can use to do this: build.sh and build-docker.sh. build.sh requires you to install the packages that are listed in the repository's README.md file, whereas build-docker.sh requires only that you have Docker already installed on your computer. I'm going to be using the Docker-based build script for the rest of this post. If you don't have Docker installed on your system, you can follow the instructions here for the community edition. ### Name your image First we need to give a name to our image, even if we use the default build. To do this, we assign a name to a variable called IMG_NAME inside a file called config that is located inside the root pi-gen folder. echo "IMG_NAME=my_name" > config  ### Build the default image Once we've named our image, we can go ahead and run the build script. ./build-docker.sh  Be prepared to wait a while when running this script; the full build took well over half an hour on my laptop and with the Docker volume located on a SSD. It also consumed several GB of space on the SSD. #### Resuming a failed build The first time I used pi-gen the build failed twice. Once, it hung without doing anything for several minutes, so I canceled it with a Ctrl-C command. The other time I encountered a hash error when installing a Debian package. We can resume a failed build from the point of failure by assigning the value 1 to the CONTINUE variable when calling build-docker.sh again. CONTINUE=1 ./build-docker.sh  If we don't want to run previously built stages, we can simply place a file inside the corresponding folder named SKIP. For example, if our build fails at stage2, we can place SKIP files inside the stage0 and stage1 folders, then rerun the build-docker.sh script with CONTINUE=1. Unfortunately, I have sometimes noticed that I have to also rebuild the stage prior to the one where the build failed. In the worst case, I had to rebuild all the stages because the fixes I applied to a file in stage2 were not accounted for when I tried to skip building stages 0 and 1. YMMV with this; I have no idea how well the SKIP mechanism works for the normal build.sh script. After a successful build, we can find our custom images located inside the deploy folder of the pi-gen directory. These may then be written onto a SD card and used as a standard Raspbian image. We can ensure that the build container is preserved even after successful builds using PRESERVE_CONTAINER=1 ./build-docker.sh  ## Custom Raspbian images Now that we've got the default build working, let's start by customizing the build process. For this post, I have the following goals: • Build only the lite version of the Raspbian images • Add a custom user account and delete the default pi account • Set the Pi's locale information In a follow-up post, I will discuss the following: • Setup the WiFi for a home network • Setup ssh so that we can log on to the Pi remotely on its first startup ### Building just Raspbian Lite Raspbian Lite is a minimal Raspbian image without the X windows server and speciality modules that would otherwise make Raspbian more user friendly. It's an ideal starting point for projects that are highly specialized, require only a few packages, and do not require a GUI. pi-gen creates Raspbian images in sequential steps called stages. At the time of this writing, there were five stages, with stages 2, 4, and 5 producing images of the operating system. Building everything from stage 0 up to and including stage 2 produces a Raspbian Lite image. We can speed up the build process and save harddrive space by disabling all the later stages. To disable the build for a particular a stage, we add an empty file called SKIP inside the corresponding stage folder of the pi-gen root directory, just as we did above when skipping previously built stages. We also disable the explicit creation of images by adding an empty file called SKIP_IMAGES to stages 4 and 5. (We don't need to add a SKIP_IMAGES file to the stage3 folder because no image is produced at this stage.) touch ./stage3/SKIP ./stage4/SKIP ./stage5/SKIP touch ./stage4/SKIP_IMAGES ./stage5/SKIP_IMAGES  Now, when we run build-docker.sh, pi-gen will only build and produce one image for Raspbian Lite in the deploy directory. ### Add a custom user account The default user in Raspbian is called pi. This account is created in stage1 in the the script stage1/01-sys-tweaks/00-run.sh. This account is not very secure because it and its password, raspberry, are the well-known defaults in Raspbian. Let's go ahead and change them. The relevant lines in the script look like this: on_chroot << EOF if ! id -u pi >/dev/null 2>&1; then adduser --disabled-password --gecos "" pi fi echo "pi:raspberry" | chpasswd echo "root:root" | chpasswd EOF  The user pi is created with the line adduser --disabled-password --gecos "" pi if it doesn't already exist. According to the adduser man pages The --disabled-password flag prevents the program passwd from setting the account's password when adduser is run, but remote logins without password authentication to the pi account are still allowed. the --gecos "" flag simply adds an empty string to the /etc/passwd file for the pi account. After the user is created, raspberry is set as pi's password and root is set as the root password in the lines echo "pi:raspberry" | chpasswd and echo "root:root" | chpasswd. Let's start by modifying the pi account. For the sake of this example, let's change its name to alphapi. For the password, we will generate a temporary, random password and write it to a file in the deploy directory. We'll do the same for root. The modifications look like the following: user_passwd=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-8}) root_passwd=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-8}) # Write passwords to a file. cat <<EOF > /pi-gen/deploy/users${user_passwd}
${root_passwd} EOF on_chroot << EOF if ! id -u alphapi >/dev/null 2>&1; then adduser --disabled-password --gecos "" alphapi fi echo "alphapi:${user_passwd}" | chpasswd
echo "root:${root_passwd}" | chpasswd EOF  The first two lines create random alphanumeric passwords for the users alphapi and root. They should be changed immediately when the image is first run. user_passwd=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-8}) root_passwd=$(< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-8})  This way of password generation works by reading random bytes from /dev/urandom and redirecting them to the standard input of the tr command, which filters the input so only alphanumeric characters remain. Next, the output is piped to the head command, which outputs only the first eight alphanumeric characters produced in this fashion. The passwords are then written to a file named users inside the deploy directory where the outputs will eventually be placed. # Write passwords to a file. cat <<EOF > /pi-gen/deploy/users${user_passwd}
${root_passwd} EOF  The remaining parts of the script are more-or-less the same as before, except I changed pi to alphapi and used variable substitution for the passwords. Running ./build-docker.sh at this point will raise an error in stage02 because it's at this stage where the user pi is added to the various groups on the system. We therefore need to open stage2/01-sys-tweaks/01-run.sh and modify the following lines, replacing pi with alphapi. for GRP in adm dialout cdrom audio users sudo video games plugdev input gpio spi i2c netdev; do adduser alphapi$GRP
done


### Set the locale information

The locale information used by your operating system may be modified as follows. Open stage0/01-locale/00-debconf. I personally changed every occurence of en_GB.UTF-8 to en_US.UTF-8, but you can set your locale accordingly.

# Locales to be generated:
# Choices: All locales, aa_DJ ISO-8859-1, aa_DJ.UTF-8 UTF-8, ...
locales locales/locales_to_be_generated multiselect en_US.UTF-8 UTF-8
# Default locale for the system environment:
# Choices: None, C.UTF-8, en_US.UTF-8
locales locales/default_environment_locale   select  en_US.UTF-8


Next, we open stage2/01-sys-tweaks/00-debconf. I currently live in Europe, so I made the following changes:

tzdata        tzdata/Areas    select  Europe


I also made the following changes to switch from the default British English to American English:

keyboard-configuration keyboard-configuration/xkb-keymap select us
keyboard-configuration keyboard-configuration/fvariant  select  English (US) - English (US\, international with dead keys)


Note that the comment in 00-debconf above the keyboard-configuration/xkb-keymap line erroneously states that American English is an option, but it's not. You need to change it from "gb" to "us" if you want the American layout.

## Using the custom image

With all these changes, we can build our new image by running ./build-docker.sh and, if successful, find a .zip file inside the deploy directory with the image name and date.

To use this image, we unzip the file to extract the .img file inside it. Next, we need to copy it onto a SD card that will plug into the pi. I have a SD card reader/writer on my laptop for which I check for its Linux device name by running lsblk before and after plugging in the card. (The device that appears in the output of lsblk after plugging it in is its name, which is /dev/mmcblk0 on my laptop). Once I get its device name, I use the Linux dd command to copy the contents of the image onto the card. (Be sure to change /dev/mccblk0 to match the name that your system gives to your SD card device.)

sudo dd if=2018-07-21-my_name-lite.img of=/dev/mmcblk0 bs=4096; sync


Please be EXTREMELY careful that you get the device name right. It's not very difficult to write the contents of the image file over your root partition or other important data.

After writing the image, we can plug the SD card into our pi, boot it up, and try logging in as alphapi with the random password that was created in the users file. Be sure at this point to change your user's and root's password. We can also verify that the keyboard was set to US English by typing Shift-3 and observing whether we get a hashtag (#) symbol and not the symbol for the British pound currency.

In a follow-up post, I will describe how to setup the network and SSH so I can continue to setup my Raspberry Pi without ever needing a terminal.

# How I built a cross-compilation workflow for the Raspberry Pi

Some of you may know I tinker with the Raspberry Pi in my free time and that one of my current projects is to build a lensless microscope with the Pi as the brains. To control the microscope, I decided a while ago that I would use Micro-Manager, an open-source software package for microscope control. I made this decision for a few reasons:

1. I already knew the Micro-Manager codebase since I use it frequently at work.
2. The Micro-Manager core provides a device-independent interface to hardware.
3. I've contributed to the project in the past and feel a sense of loyalty to the project and the people involved. Expanding Micro-Manager into embedded microscopy would be a great way for me to give back to the community.

Building Micro-Manager from source code presents its own set of challenges. After ensuring that you have the correct build environment, you need to actually compile it, and here's where things get tricky in Raspyberry Pi development. The Pi has an ARM processor, whereas most laptops and workstations use a x86_64 processor. This means that code compiled on a typical desktop PC will not work on the Pi. As I showed in my earlier post, you can compile the code directly on the Pi to circumvent this, but this unfortunately is quite cumbersome because the code base and dependencies are quite large. (They are nearly 8 GB in total). Furthermore, compiling the project on the Pi is slow and requires connecting to it via ssh or working directly on a TV screen or monitor.

These problems extend beyond Micro-Manager to other large-scale projects that require code compilation for a specific processor architecture. In this post, I'll describe the workflow that I developed for cross-compiling projects for the Raspberry Pi.

## Previous attempts

Prior to the workflow that is the main topic of this post, I managed to cross-compile Micro-Manager using a chroot environment and the QEMU emulator. chroot is a Linux command that changes the apparent root (or '/') directory for a running process. With this approach, I mount an image of the Raspbian operating system that contains the gcc and g++ compilers and libraries for the ARM architecture. Then, I chroot into the image and run a setup script that builds the software. During execution of this script, the QEMU static libraries run the ARM compilers from within the chroot environment to build the project. The compiled code remains inside the image, which I then burn onto a micro SD card to insert into the Pi. I uploaded a gist of the bash script which orchestrates all this, and my inspiration for this approach came from a great series of blog posts from Disconnected Systems.

Ultimately this approach is a huge amount of work. As you can see in the gist, it's fairly complicated bash scripting that's not easy to debug. Furthermore, the setup script that is run inside the image needs to do a lot of work beyond cross-compiling, like setting up the user, permissions, network, etc. Debugging the final product is also a challenge because you need to verify that it's working on the Pi, which requires burning the image to a micro SD card.

## Cross-compiling with Docker

After a bit of research I decided I would try instead to use Docker for cross-compilation and deployment to the Pi. I had just started using Docker at work to build reproducible environments for scientific computing research. In particular, and unlike my chroot script, I had learned that a Docker container that built the project could work on nearly any system that had Docker installed. Furthermore, deploying updates can be done on any Raspberry Pi that's running Docker.

I liked the idea of a portable cross-compilation workflow, so I dove into the Docker documentation and managed to get everything working in a few weeks of tinkering at home.

### An overview of Docker

You can find many resources online about Docker, so I won't go into the details here. The main thing you need to know is that Docker is a system for creating, running, and sharing containers, which are something like light weight virtual machines. Containers solve the problem in software development of how to build and deploy programs that have a complex set of dependencies. It does this by isolating the environment in which a program runs from the rest of the operating system. For example, if you have a computer that has a certain version of gcc (the GNU C compiler) installed, but your application requires a different version, then you can install the required gcc along with your application inside a container and they will not interfere with the version of gcc that belongs to your operating system. This also means that you can send your container to any machine that has Docker installed and it should just run without having to do any setup.

Other important things to know about Docker are:

• There are two main types of objects: images and containers. Images are sort of like blueprints that define what is inside a container, whereas containers are like the actual buildings specified by the blueprints. There can be many containers that come from a single image.
• Containers are meant to be immutable. When you stop them and restart them, they always restart in the same state as when they were first created.
• Since containers are immutable, some of your application data may need to be placed in a volume, which is either another container or a folder on the host system. A volume gets connected to your application container and exists even when your application container is not running.

## The cross-compilation workflow

Now that we have established the essential background to this project, let's look at the cross-compilation workflow. Below is a picture that provides a sense of the entire process, moving in general from left-to-right.

The process involves two Docker containers: one for building Micro-Manager and the other for running the application. The build dependencies and the QEMU emulator are both located inside the build container, having been specified when its image was created. These allow us to compile Micro-Manager for the ARM architecture. The source code is connected to the build container as a bind mount, which is a folder from the host workstation that is mounted inside the build container when it is run.

Once the libraries are compiled, they are installed into a folder inside the bind mount so that the host system will have access to them after the build container closes. Next, the compiled libraries are copied directly into an image that defines the application container. This image defines only the essential run-time requirements for running Micro-Manager and nothing else. The application image is stored on the registry server which I set up on my local network. This makes it easy for the Raspberry Pi to download the latest image and run the Micro-Manager application container whenever I make changes.

An important aspect of this workflow is how the data is passed between the systems and containers. Unlike what you will find in many introductory tutorials on Docker, I do not add the Micro-Manager source code directly to the build image/containers but instead use a bind mount. The reason for this is that the source code and 3rd party libraries are quite large, about 8 GB in total. By using a bind mount, I avoid needless copying of this data. Another reason for using a bind mount is that the source code will change frequently during development. If I add the source code to the image, then I will have to recreate the image every time the source code changes.

Once the libraries are built, I directly copy them into the application image because they are much, much smaller than the source code. I also want the code stored directly in the image so that the application image is all the Raspberry Pi needs to run the program. The image is stored in my local Docker registry server so that once I push an updated image to the server, the Raspberry Pi can download it and use it immediately.

### Step 0: Prerequisites

I am going to assume that you already have installed Docker. (If not, follow these directions.) I am also going to assume that you are somewhat familiar with how to work on a Linux system. The Raspberry Pi runs Linux, so you probably wouldn't be here if you didn't already know at least a little.

For this article, I am working with these versions of Docker and Ubuntu on my host workstation.:

kmdouglass@xxxxx:~$uname -a Linux xxxxx 4.13.0-39-generic #44~16.04.1-Ubuntu SMP Thu Apr 5 16:43:10 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux kmdouglass@xxxxx:~$ docker version
Client:
Version:      18.03.1-ce
API version:  1.37
Go version:   go1.9.5
Git commit:   9ee9f40
Built:        Thu Apr 26 07:17:20 2018
OS/Arch:      linux/amd64
Experimental: false
Orchestrator: swarm

Server:
Engine:
Version:      18.03.1-ce
API version:  1.37 (minimum version 1.12)
Go version:   go1.9.5
Git commit:   9ee9f40
Built:        Thu Apr 26 07:15:30 2018
OS/Arch:      linux/amd64
Experimental: false


Finally, below is how my project directory structure is laid out.:

kmdouglass@xxxxx:~/src/alphapi/docker$tree -L 2 . └── rpi-micromanager ├── 2.0-python │ ├── build │ └── Dockerfile └── build ├── build ├── Dockerfile ├── run └── setup  I have two folders; build, which contains the files for the build container, and 2.0-python, which contains the files for creating the Micro-Manager application container. (In my case, I am going to build the Python wrapper for Micro-Manager 2.0.) Inside each folder are the scripts and Dockerfiles that execute the various steps of the workflow. The final prerequisite is to register QEMU with the Docker build agent. First, install a few packages for QEMU. On Ubuntu, this looks like $ sudo apt update
$sudo install qemu qemu-user-static qemu-user binfmt-support  Finally, register the build agent with the command: $ docker run --rm --privileged multiarch/qemu-user-static:register --reset


### Step 1: Create the build image

Inside the build folder, I have a file called Dockerfile. Here are its contents.

# Copyright (C) 2018 Kyle M. Douglass
#
# Defines a build environment for Micro-Manager on the Raspberry Pi.
#
# Usage: docker build \
#          -t NAME:TAG \
#         .
#

FROM resin/raspberrypi3-debian:stretch
MAINTAINER Kyle M. Douglass <kyle.m.douglass@gmail.com>

RUN [ "cross-build-start" ]

# Get the build dependencies.
RUN apt-get update && apt-get -y install --no-install-recommends \
autoconf \
automake \
build-essential \
git \
libatlas-base-dev \
libboost-dev \
libboost-all-dev \
libtool \
patch \
pkg-config \
python3-dev \
python3-pip \
python3-setuptools \
python3-wheel \
swig \
&& apt-get clean && rm -rf /var/lib/apt/lists/* \
&& pip3 install numpy

RUN [ "cross-build-end" ]

# Set up the mount point for the source files and setup script.
VOLUME /micro-manager/src

WORKDIR /micro-manager/src
ENTRYPOINT [ "/sbin/tini", "-s", "--" ]
CMD [ "/micro-manager/setup" ]


A Dockerfile defines the steps in building an image -- in this case, the build image. Let's break this file down into pieces. In the first two lines that follow the comments, I specify that my image is based on the resin/raspberrypi3-debian:stretch image and that I am the maintainer.

FROM resin/raspberrypi3-debian:stretch
MAINTAINER Kyle M. Douglass <kyle.m.douglass@gmail.com>


Images from Resin are freely available and already have the QEMU emulator installed. Next, I specify what commands should be run for the ARM architecture. Any commands located between RUN [ "cross-build-start" ] and RUN [ "cross-build-end" ] will be run using the emulator. Inside these two commands, I install the build dependencies for Micro-Manager using apt-get and pip. (These are just standard commands for installing software on Debian/Ubuntu Linux machines and from PyPI, respectively.)

After the installation of the requirements completes, I add the setup script to the folder /micro-manager inside the image with the ADD setup /micro-manager/ command. The setup script contains the commands that will actually compile Micro-Manager. I then define a mount point for the source code with VOLUME /micro-manager/src. It's important to realize here that you do not mount volumes inside images, you mount volumes inside containers. This command is just telling the image to expect a folder to be mounted at this location when the container is run.

The last three lines set the working directory, the entrypoint and the default container command, respectively.

WORKDIR /micro-manager/src
ENTRYPOINT [ "/sbin/tini", "-s", "--" ]
CMD [ "/micro-manager/setup" ]


This specific entrypoint tells Docker that any containers built from this image should first run Tini, which is a lightweight init system for Docker containers. If you do not specify Tini as the entry point, then it will not be able to reap zombies. (I don't know what this means exactly, but it sounds cool and you can read about it here: https://github.com/krallin/tini)

By default, the container will run the setup script, but, since I used the CMD directive, this can be overriden in case we need to perform some manual steps. Roughly speaking, you can think of the entrypoint as the command that can not be overridden and the CMD command as the one that can be. In other words, Tini will always be executed when containers created from this image are launched, whereas you can choose not to run the setup script but instead to enter the container through a Bash shell, for example.

To build the image, I use the following build script located in the same directory as the Dockerfile for convenience.

#!/bin/bash
# Copyright (C) 2018 Kyle M. Douglass
#
# Usage: ./build
#

docker build \
-t localhost:5000/rpi-micromanager:build \
.


By using -t localhost:5000/rpi-micromanager:build argument I am giving the image a name of rpi-micromanager, a tag of build, and specifying that I will eventually host this image on my local registry server (localhost) on port 5000.

In case you are wondering about the contents of the setup script, don't worry. I'll explain it in the next section.

### Step 2: Compile Micro-Manager

After the image is built, I create a container and use it to compile Micro-Manager. For this, I use the run script in the build directory.

#!/bin/bash
# Copyright (C) 2018 Kyle M. Douglass
#
# Usage: ./run DIR CONFIGURE
#
# DIR is the parent folder containing the micro-manager Git
# repository, the 3rdpartypublic Subversion repository, and any
#
# If CONFIGURE=true, the build system is remade and the configure
# script is rerun before running 'make' and 'make install'. If
# CONFIGURE=false, only 'make' and 'make install' are run.
#
# The compiled program files are stored in a bind mount volume so that
# they may be copied into the deployment container.
#

src_dir=$1 cmd="/micro-manager/setup$2"

# Remove the build artifacts from previous builds.
if [ "$2" == true ] || [ "$2" == false ]; then
rm -rf ${src_dir}/build || true fi docker run --rm \ -v${src_dir}:/micro-manager/src \
--name mm-build \
localhost:5000/rpi-micromanager:build \
${cmd}  The script takes two arguments. The first is the path to the folder containing all the source code (see below for details). The second argument is either true or false. (It can actually be anything, but it will only compile Micro-Manager if either true or false are provided.) If true, the full build process is run, including setting up the configure script; if false, only make and make install are run, which should recompile and install only recently updated files. The run script uses the -v argument to docker run to mount the source directory into the container at the point specified by the VOLUME command in the Dockerfile. The directory layout on my host file system for the source directory looks like this: kmdouglass@xxxxx:/media/kmdouglass/Data/micro-manager$ tree -L 1
.
├── 3rdpartypublic
├── micro-manager
└── patches


The patches folder is not necessary and only there to fix a bug in the WieneckeSinscke device adapter. (This bug may be fixed by now.) 3rdpartypublic is the large Subversion repository of all the required software to build Micro-Manager, and micro-manager is the cloned GitHub repository. Prior to building, I checkout the mm2 branch because I am interested in developing my application for Micro-Manager 2.0.

The setup script that is run inside the container and mentioned in the previous section looks like this.

#!/bin/bash
#
# # Copyright (C) 2018 Kyle M. Douglass
#
# Builds Micro-Manager.
#
# Usage: ./setup CONFIGURE
#
# If CONFIGURE=true, the build system is remade and the configure
# script is rerun before running 'make' and 'make install'. If
# CONFIGURE=false, only 'make' and 'make install' or run.
#
# Kyle M. Douglass, 2018
#

# Move into the source directory.
cd micro-manager

# Undo any previous patches.

# Patch the broken WieneckeSinske device adapter.

# Compile MM2.
if [ "$1" = true ]; then # Remake the entire build system, then compile from scratch. ./autogen.sh PYTHON="/usr/bin/python3" ./configure \ --prefix="/micro-manager/src/build" \ --with-python="/usr/include/python3.5" \ --with-boost-libdir="/usr/lib/arm-linux-gnueabihf" \ --with-boost="/usr/include/boost" \ --disable-java-app \ --disable-install-dependency-jars \ --with-java="no" make make install chmod -R a+w /micro-manager/src/build elif [ "$1" = false ]; then
# Only recompile changed source files.
make
make install
chmod -R a+w /micro-manager/src/build
else
echo "$1 : Unrecognized argument." echo "Pass \"true\" to run the full build process." echo "Pass \"false\" to run only \"make\" and \"make install\"." fi  Most important in this script is the call to configure. You can see that the compiled libraries and Python wrapper will be written to the build folder inside the mounted directory. This gives the host file system access to the compiled artifacts after the container has stopped. ### Step 3: Build the application image Once the libraries are compiled, we can add them to an application image that contains only the essentials for running Micro-Manager. For this, I use a separate Dockerfile inside the 2.0-python directory. # Copyright (C) 2018 Kyle M. Douglass # # Builds the Micro-Manager 2.0 Python wrapper for the Raspberry Pi. # # Usage: docker build \ # -t NAME:TAG \ # . # FROM resin/raspberrypi3-debian:stretch MAINTAINER Kyle M. Douglass <kyle.m.douglass@gmail.com> RUN [ "cross-build-start" ] # Install the run-time dependencies. RUN apt-get update && apt-get -y install --no-install-recommends \ libatlas-base-dev \ libboost-all-dev \ python3-pip \ python3-setuptools \ python3-wheel \ && pip3 install numpy \ && apt-get clean && rm -rf /var/lib/apt/lists/* # Copy in the Micro-Manager source files. RUN useradd -ms /bin/bash micro-manager WORKDIR /home/micro-manager/app COPY --chown=micro-manager:micro-manager . . RUN [ "cross-build-end" ] # Final environment configuration. USER micro-manager:micro-manager ENV PYTHONPATH /home/micro-manager/app/lib/micro-manager ENTRYPOINT ["/sbin/tini", "-s", "--"] CMD ["/usr/bin/python3"]  As before, I use a clean resin base image. However, this time I only install the essential software to run Micro-Manager. After apt-getting and pip-installing everything, I create a new user called micro-manager and a new folder called app inside this user's home directory. # Copy in the Micro-Manager source files. RUN useradd -ms /bin/bash micro-manager WORKDIR /home/micro-manager/app  Next, I directly copy the compiled libraries into the image with the COPY command. COPY --chown=micro-manager:micro-manager . .  The two periods (.) mean that I copy the current host directory's contents into the container's current working directory (/home/micro-manager/app). What is the current host directory? Well, as I explain below, I actually run this Dockerfile from inside the build folder that was created to hold the compiled libraries in the previous step. But first, I'll end my explanation of the Dockerfile by saying that I switch the USER so that I do not run the container as root, add the library to the PYTHONPATH environment variable, and setup the default command as the python3 interpreter. To build this image, I use the following build script. #!/bin/bash # Copyright (C) 2018 Kyle M. Douglass # # Usage: ./build DIR # # DIR is the root directory containing the Micro-Manager build # artifacts. These artifacts will be added to the Docker image. # src_dir=$1

cp Dockerfile ${src_dir} cd${src_dir}

docker build \
-t localhost:5000/rpi-micromanager:2.0-python \
.


This script takes one argument, which is the build directory containing the compiled source code. The script first copies the Dockerfile into this directory and then changes into it with the cd command. (This explains the two periods (.) in the COPY command in the Dockerfile.)

Finally, I build the image and give it a name of localhost:5000/rpi-micromanager:2.0-python.

### Step 4: Add the image to the local registry server

Now we need a way to get the image from the workstation onto the Raspberry Pi. Of course, I could manually transfer the file with a USB stick or possibly use ssh, but what if I have multiple Pi's? This process could become cumbersome. Docker provides a few ways to push and pull images across a network. The most obvious is Dockerhub, a site for freely sharing images. For the moment I don't want to use Dockerhub, though, because I have not yet checked all the software licenses and am unsure as to what my rights are for putting an image with Micro-Manager software on a public repository.

A better option, especially for testing, is to use a local registry server. This server operates only on my home network and already allows my workstation and Pi's to communicate with one another. Following the official registry documentation and this blog post by Zachary Keeton, I managed to setup the registry as follows.

#### Host setup

First, we need to setup a transport layer security (TLS) certificate. It's possible to run the server without one if you don't expect your network to be attacked, but it's good practice so let's create one.

To do this, I edit the /etc/ssl/openssl.cnf file and add the following to the top of the [ v3_ca ] section.:

subjectAltName = IP:192.168.XXX.XXX


where the IP address is the address of the workstation on the network. Next, I actually create the certificate. I make a directory called certs inside my workstation home directory and then use openssl to make the cerficate. During the prompts, I press ENTER at every step except the FQDN (fully qualified domain name). For the FQDN, I enter the same IP address as above.

mkdir certs
openssl req -newkey rsa:4096 -nodes -sha256 \
-keyout certs/domain.key -x509 -days 365 \
-config /etc/ssl/openssl.cnf -out certs/domain.crt


I had to add the -config /etc/ssl/openssl.cnf argument for the subject alternative name to be added to the certificate. This part was tricky, because if this argument is not included, then the key generation step will use some other .cnf file (I am not sure which). This results in the following SAN error when attemptingt to connect to the registry.:

cannot validate certificate for 192.168.XXX.XXX because it doesn't contain any IP SANs


After the domain.key and domain.crt files have been created, I run the official registry server container. (See how handy Docker containers are? There's no messy installation beyond grabbing the container.)

docker run -d -p 5000:5000 \
--restart=always \
--name registry \
-v $(pwd)/certs:/certs \ -e REGISTRY_HTTP_TLS_CERTIFICATE=/certs/domain.crt \ -e REGISTRY_HTTP_TLS_KEY=/certs/domain.key \ registry:2  If the registry:2 image is not already downloaded, then it will be downloaded for automatically when running the container. Note that the -p 5000:5000 argument indicates that the server is using port 5000 on both the host system and inside the container. Note also that the certs directory is relative to the current directory because I use the ($pwd) command. You can change this to an absolute path if you wish on your setup.

Let's go ahead and push the application image to the server now that it's running.

docker push localhost:5000/rpi-micromanager:2.0-python


#### Setup the Pi

Now, startup the Pi. I will assume that you have already installed Docker on it and know how to communicate with it via ssh and copy files to it using scp.

I copy the certificate from the host with scp.

sudo mkdir -p /etc/docker/certs.d/192.168.XXX.XXX:5000/
sudo scp kmdouglass@192.168.XXX.XXX:/home/kmdouglass/certs/domain.crt /etc/docker/certs.d/192.168.XXX.XXX:5000/ca.crt


The IP address that I am using is the one to the machine where the registry server is running. After this step, I make the operating system trust the certificate.

sudo scp kmdouglass@192.168.XXX.XXX:/home/kmdouglass/certs/domain.crt /usr/local/share/ca-certificates/192.168.XXX.XXX.crt
sudo update-ca-certifications


Finally, I restart the Docker daemon.

sudo service docker restart


If everything is working, then I should be able to pull the image from your network's registry server.

docker pull 192.168.XXX.XXX:5000/rpi-micromanager:python2.0


### Step 5: Run Micro-Manager!

And now the moment of truth: running the application container. Since it's setup to run Python automatically, I use a pretty simple docker run command.

docker run -it --rm \
--name micro-manager \
192.168.XXX.XXX:5000/rpi-micromanager:2.0-python


I verify that the Micro-Manager Python wrapper is working by trying to import it and run a few basic commands.

>>> import MMCorePy
>>> mmc = MMCorePy.CMMCore()
>>> mmc.getVersionInfo()


If these work without error, then congratulations! You're now ready to start building your embedded microscopy system ;)

### Step 6: Running the whole process

The beauty of having scripted all these steps is that the full workflow may be executed quite simply. From the host system's build folder, run:

kmdouglass@xxxxx:~/src/alphapi/docker/rpi-micromanager/build$./build kmdouglass@xxxxx:~/src/alphapi/docker/rpi-micromanager/build$ ./run /path/to/source true


From the 2.0-python folder:

kmdouglass@xxxxx:~/src/alphapi/docker/rpi-micromanager/2.0-python ./build /path/to/source/artifacts
kmdouglass@xxxxx:~$docker push localhost:5000/rpi-micromanager:2.0-python  And from the Raspberry Pi: pi@yyyyy:~$ docker pull 192.168.XXX.XXX:5000/rpi-micromanager:2.0-python
pi@yyyyy:~$docker run -it --rm \ --name micro-manager \ 192.168.XXX.XXX:5000/rpi-micromanager:2.0-python  Hopefully this is enough to get you started building Micro-Manager for the Raspberry Pi with Docker. Though I focused on Micro-Manager, the workflow should be generally applicable to any large scale project in which you want to isolate the build environment from the host machine. If you have any questions, just leave them in the comments. Happy programming! # Implementing a fast Gibson-Lanni PSF solver in Python Many techniques in modern fluorescence microscopy--such as deconvolution and single molecule localization microscopy--rely on the computation of accurate microscope point spread functions (PSFs). Several models exist for these purposes with varying degrees of accuracy and generality. One such model, the so-called Gibson-Lanni model, approximates the PSF of an immersion microscope objective by accounting for the different refractive indexes of the immersion medium, coverslip, and sample, as well as variations in the thicknesses of the different layers. This post describes a Python implementation of a fast computational approach to the G&L PSF that was presented in Fast and accurate three-dimensional point spread function computation for fluorescence microscopy by Li, Xue, and Blu. The approach is fast because it avoids the need to perform any explicit integration of the Kirchhoff diffraction integral, such as is done in PSF Generator. The prototype is based on the manuscript and the associated MATLAB code at http://www.ee.cuhk.edu.hk/~tblu/monsite/phps/fastPSF.php ## References¶ In [1]: import sys %pylab inline import scipy.special from scipy.interpolate import interp1d from matplotlib import animation plt.style.use('dark_background') plt.rcParams['figure.facecolor'] = '#272b30' plt.rcParams['image.cmap'] = 'viridis' print('Python {}\n'.format(sys.version)) print('NumPy\t\t{}'.format(np.__version__)) print('matplotlib\t{}'.format(matplotlib.__version__)) print('SciPy\t\t{}'.format(scipy.__version__))  Populating the interactive namespace from numpy and matplotlib Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:53:06) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] NumPy 1.13.3 matplotlib 2.1.0 SciPy 0.19.1  ## Simulation setup¶ ### Define the simulation parameters¶ The Gibson-Lanni PSF model accounts for differences between design parameters and real parameters that describe the fluorescence microscope, such as the refractive indexes and thicknesses of the immersion medium, coverslip, and sample. For more information, please see the above references or, if you do not have access to the publications, the description of the model here: http://bigwww.epfl.ch/algorithms/psfgenerator/ In [2]: # Image properties # Size of the PSF array, pixels size_x = 256 size_y = 256 size_z = 128 # Precision control num_basis = 100 # Number of rescaled Bessels that approximate the phase function num_samples = 1000 # Number of pupil samples along radial direction oversampling = 2 # Defines the upsampling ratio on the image space grid for computations # Microscope parameters NA = 1.4 wavelength = 0.610 # microns M = 100 # magnification ns = 1.33 # specimen refractive index (RI) ng0 = 1.5 # coverslip RI design value ng = 1.5 # coverslip RI experimental value ni0 = 1.5 # immersion medium RI design value ni = 1.5 # immersion medium RI experimental value ti0 = 150 # microns, working distance (immersion medium thickness) design value tg0 = 170 # microns, coverslip thickness design value tg = 170 # microns, coverslip thickness experimental value res_lateral = 0.1 # microns res_axial = 0.25 # microns pZ = 2 # microns, particle distance from coverslip # Scaling factors for the Fourier-Bessel series expansion min_wavelength = 0.436 # microns scaling_factor = NA * (3 * np.arange(1, num_basis + 1) - 2) * min_wavelength / wavelength  ### Create the coordinate systems¶ In [3]: # Place the origin at the center of the final PSF array x0 = (size_x - 1) / 2 y0 = (size_y - 1) / 2 # Find the maximum possible radius coordinate of the PSF array by finding the distance # from the center of the array to a corner max_radius = round(sqrt((size_x - x0) * (size_x - x0) + (size_y - y0) * (size_y - y0))) + 1; # Radial coordinates, image space r = res_lateral * np.arange(0, oversampling * max_radius) / oversampling # Radial coordinates, pupil space a = min([NA, ns, ni, ni0, ng, ng0]) / NA rho = np.linspace(0, a, num_samples) # Stage displacements away from best focus z = res_axial * np.arange(-size_z / 2, size_z /2) + res_axial / 2  ## Step 1: Approximate the pupil phase with a Fourier-Bessel series¶ z.reshape(-1,1) flips z from a row array to a column array so that it may be broadcast across rho. The coefficients C are found by a least-squares solution to the equation \begin{equation*} \mathbf{\phi} \left( \rho , z \right)= \mathbf{J} \left( \rho \right) \mathbf{c} \left( z \right) \end{equation*}$ \mathbf{c} $has dimensions num_basis$ \times $len(z). The J array has dimensions num_basis$ \times $len(rho) and the phase array has dimensions len(z)$ \times $len(rho). The J and phase arrays are therefore transposed to get the dimensions right in the call to np.linalg.lstsq. In [4]: # Define the wavefront aberration OPDs = pZ * np.sqrt(ns * ns - NA * NA * rho * rho) # OPD in the sample OPDi = (z.reshape(-1,1) + ti0) * np.sqrt(ni * ni - NA * NA * rho * rho) - ti0 * np.sqrt(ni0 * ni0 - NA * NA * rho * rho) # OPD in the immersion medium OPDg = tg * np.sqrt(ng * ng - NA * NA * rho * rho) - tg0 * np.sqrt(ng0 * ng0 - NA * NA * rho * rho) # OPD in the coverslip W = 2 * np.pi / wavelength * (OPDs + OPDi + OPDg) # Sample the phase # Shape is (number of z samples by number of rho samples) phase = np.cos(W) + 1j * np.sin(W) # Define the basis of Bessel functions # Shape is (number of basis functions by number of rho samples) J = scipy.special.jv(0, scaling_factor.reshape(-1, 1) * rho) # Compute the approximation to the sampled pupil phase by finding the least squares # solution to the complex coefficients of the Fourier-Bessel expansion. # Shape of C is (number of basis functions by number of z samples). # Note the matrix transposes to get the dimensions correct. C, residuals, _, _ = np.linalg.lstsq(J.T, phase.T)  ### Compare the function to its Fourier-Bessel expansion¶ In [5]: # Which z-plane to compute z0 = 24 # The Fourier-Bessel approximation est = J.T.dot(C[:,z0]) fig, ax = plt.subplots(ncols=2, sharey=True, figsize=(10,5)) ax[0].plot(rho, np.real(phase[z0, :]), label=r'$ \exp{ \left[ jW \left( \rho \right) \right] }$') ax[0].plot(rho, np.real(est), '--', label='Fourier-Bessel') ax[0].set_xlabel(r'$\rho$') ax[0].set_title('Real') ax[0].legend(loc='upper left') ax[1].plot(rho, np.imag(phase[z0, :])) ax[1].plot(rho, np.imag(est), '--') ax[1].set_xlabel(r'$\rho$') ax[1].set_title('Imaginary') ax[1].set_ylim((-1.5, 1.5)) plt.show()  ## Step 2: Compute the PSF¶ Here, we use the Fourier-Bessel series expansion of the phase function and a Bessel integral identity to compute the approximate PSF. Each coefficient$ c_{m} \left( z \right) $needs to be multiplied by \begin{equation*} R \left(r; \mathbf{p} \right) = \frac{\sigma_m J_1 \left( \sigma_m a \right) J_0 \left( \beta a \right)a - \beta J_0 \left( \sigma_m a \right) J_1 \left( \beta a \right)a }{\sigma_m^2 - \beta^2} \end{equation*} and the resulting products summed over the number of basis functions.$ \mathbf{p} $is the parameter vector for the Gibson-Lanni model,$ \sigma_m $is the scaling factor for the argument to the$ m'th $Bessel basis function, and$ \beta = kr\text{NA} $. b is defined such that R has dimensions of len(r)$ \times $len(rho). In [6]: b = 2 * np. pi * r.reshape(-1, 1) * NA / wavelength # Convenience functions for J0 and J1 Bessel functions J0 = lambda x: scipy.special.jv(0, x) J1 = lambda x: scipy.special.jv(1, x) # See equation 5 in Li, Xue, and Blu denom = scaling_factor * scaling_factor - b * b R = (scaling_factor * J1(scaling_factor * a) * J0(b * a) * a - b * J0(scaling_factor * a) * J1(b * a) * a) R /= denom  Now compute the point-spread function via \begin{equation*} PSF \left( r, z; z_p, \mathbf{p} \right) = \left| \mathbf{R} \left( r; \mathbf{p} \right) \mathbf{c} \left( z \right) \right|^2 \end{equation*} In [7]: # The transpose places the axial direction along the first dimension of the array, i.e. rows # This is only for convenience. PSF_rz = (np.abs(R.dot(C))**2).T # Normalize to the maximum value PSF_rz /= np.max(PSF_rz)  ### Profile in r and z¶ In [8]: fig, ax = plt.subplots() ax.imshow(PSF_rz, extent=(r.min(), r.max(), z.max(), z.min())) ax.set_xlim((0,2.5)) ax.set_ylim((-6, 0)) ax.set_xlabel(r'r,$\mu m$') ax.set_ylabel(r'z,$\mu m$') plt.show()  z is the stage displacement in an inverted microscope. So, negative z's correspond to moving "up" in the sample. ## Step 3: Resample the PSF onto a rotationally-symmetric Cartesian grid¶ Here we generate a two dimensional grid where the value at each grid point is the distance of the point from the center of the grid. These values are supplied to an interpolation function computed from PSF_rz to produce a rotationally-symmetric 2D PSF at each z-position. In [9]: # Create the fleshed-out xy grid of radial distances from the center xy = np.mgrid[0:size_y, 0:size_x] r_pixel = np.sqrt((xy[1] - x0) * (xy[1] - x0) + (xy[0] - y0) * (xy[0] - y0)) * res_lateral PSF = np.zeros((size_y, size_x, size_z)) for z_index in range(PSF.shape[2]): # Interpolate the radial PSF function PSF_interp = interp1d(r, PSF_rz[z_index, :]) # Evaluate the PSF at each value of r_pixel PSF[:,:, z_index] = PSF_interp(r_pixel.ravel()).reshape(size_y, size_x)  ## Save z-stack to a movie¶ In [10]: fig, ax = plt.subplots(nrows=1, ncols=1) # Rescale the PSF values logarithmically for better viewing PSF_log = np.log(PSF) vmin, vmax = PSF_log.min(), PSF_log.max() img = ax.imshow(PSF[:,:,64], vmin=vmin, vmax=vmax) img.set_extent([-r.max(), r.max(), -r.max(), r.max()]) txt = ax.text(3, 7, 'z = {:.1f}$\mu m$'.format(z[64])) ax.set_xlim((-8, 8)) ax.set_xticks((-5, 0, 5)) ax.set_xlabel(r'x,$\mu m$') ax.set_ylim((-8, 8)) ax.set_yticks((-5, 0, 5)) ax.set_ylabel(r'y,$\mu m$') ax.spines['top'].set_visible(False) ax.spines['bottom'].set_visible(False) ax.spines['left'].set_visible(False) ax.spines['right'].set_visible(False) # Initialize the figure with an empty frame def init(): img.set_data(np.zeros((size_y, size_x))) return img, # This function is called for each frame of the animation def animate(frame): img.set_data(np.log(PSF[:, :, frame])) txt.set_text('z = {:.1f}$\mu m$'.format(z[frame])) return img, # Create the animation anim = animation.FuncAnimation(fig, animate, frames=len(z), init_func=init, interval=20, blit=True) # Save the animation myWriter = animation.FFMpegWriter(fps=10, extra_args=['-vcodec', 'libx264']) anim.save('gibson-lanni.mp4', writer = myWriter) plt.close()  ## Summary¶ In summary, this method for calculating the Gibson-Lanni PSF is fast because it reduces the problem to a numer of matrix operations, rather than a numerical integration of the Kirchhoff diffraction integral. I especially find the Fourier-Bessel approximation of the phase function very clever, since this enables us to apply the integral identity described above. Moreover, it seems like the approach can extend to computing PSFs from other wavefront aberrations, though at the moment I do not know how it might handle non-rotationally symmetric pupils. (I am referring to the W variable above.) I would like to thank the first author of the work, Jizhou Li, for encouraging me to write this as a blog post and for providing feedback on the implementation presented here. # Accessing the Raspberry Pi camera image sensor WARNING You can easily ruin your Raspberry Pi camera module by following the steps in this post. Proceed with caution. Over the past half year I have been making slow but steady progress on my lensless imager project. The purpose, aside from having a bit of fun, is to create an imaging system for basic cell biology that doesn't use an expensive microscope objective. A lensless imager works just as its name implies: an image sensor records the scattered light from a microscopic, transparent object and computationally reconstructs an image of that object, all without a lens. The best resolutions are achieved when the object is relatively close to the image sensor. Ideally, the separation between the object and the sensor's pixels would be at most about one millimeter. This limit is partly determined by the light source's spatial coherence, but also by the fact that high resolution is achieved by recording the scattered light at very large angles, which is possible only when the sample is close to the sensor. Today I had a bit of free time so I decided to see whether I could remove the housing that surrounds the Raspberry Pi camera's sensor. The Raspberry Pi Camera Module version 2 sensor is a Sony IMX219 color chip. Directly above the sensor is a filter, a lens, and the housing for both of these that prevent me from placing anything closer than about half a centimeter from the sensor plane. If I would want to use this camera for the lensless imager, then the housing would have to go. Now, even without the housing the Raspberry Pi camera is not necessarily the best option for the project because the IMX219 is a color sensor. This means that there is a Bayer filter over its pixels, which would cut the resolution of the imager since I would be using a very narrow band light source. Effectively, only a quarter of the pixels would be receiving any light. Regardless, I had a spare second camera and it interfaces well with the Raspberry Pi, so I figured it would make for a good prototype. As you will see, I did slightly damage my sensor, though it seems to still work. You can easily ruin your camera module or cut your finger by following these steps, so proceed at your own risk. ## Step 0: The Raspberry Pi Camera Module V2 In the picture below you see my Raspberry Pi Camera Module. From above, you can see the small circular aperture with the lens immediately behind it. The sensor is inside the small gray rectangular housing that is attached to the control board by a small ribbon cable (to its right) and a bit of two-sided sticky foam tape (underneath the sensor; not visible). ## Step 1: Remove the main ribbon cable To make working on the board a bit easier, I removed the white ribbon cable that attaches the module to the Pi. I did this by pulling on the black tabs on the two ends of the connecter until the cable is easily removed. I labeled the sides of the ribbon cable just in case. ## Step 2: Detach the sensor's ribbon cable Next, I used my finger and thumb nail to remove the small ribbon cable that attaches the sensor to the control board. I essentially applied a small torque to the bottom edge of the connector until it just "popped" up, as seen in the second image below. ## Step 3: Remove the sensor from the control board In the third step, I used my thumbnail to gently pry the sensor from the control board. The sensor is attached with some two-sided sticky tape and may need a few minutes of work to come free. ## Step 4: Remove the rectangular housing In this step you risk cutting your finger, so please be careful. The housing around the sensor is glued. To remove it, you will need to gently work a knife (or, better yet, a thin screw driver) between the housing and the sensor board, taking care not to let the blade go too far into the housing and possibly ruining one of the resistors or wire bonds. Once you get a knife between the two, try popping the housing off of the sensor. When I did this I cut on three sides of the housing, but in retrospect I should have only cut on the side opposite the ribbon cable and pried the other sides loose. This is because I damaged a small resistor when the knife blade went too far into the housing. You can see this below and, at the same time, get an idea of the layout of the sensor board so you know where you can and can't cut. If you have the normal version of the camera, then you can also find the IR blocking filter inside the housing. Fortunately for me the camera still works, despite the damaged resistor. I can now place samples directly on the sensor if I wanted to, though the wire bonds from the sensor to its control board appear quite fragile. For this reason, it may make more sense to build a slide holder that holds a sample just above the surface without touching it. For now, I can use this exposed sensor to prototype different methods for mounting the sample. # Modeling noise for image simulations In my previous post, I described a method for simulating inline holography images. The ultimate purpose of doing this was to generate holography data that could be used to test the performance of different reconstruction algorithms. Since I would know the input object, I could apply the reconstruction algorithm to the holograms and see how closely the reconstructed object matched the known input. My modeling however ignored an important aspect about the holographic process, namely the acquisition of digital images and the assoicated noise that would accompany the raw data. This is important because holographic reconstruction algorithms need to be robust against the uncertainty that will inevitably be introduced by recording the hologram with a digital camera. In [1]: %pylab inline import scipy from numpy.fft import fft2, fftshift, ifftshift from mpl_toolkits.axes_grid1 import make_axes_locatable from matplotlib import animation plt.style.use('dark_background') plt.rcParams['figure.facecolor'] = '#272b30' plt.rcParams['image.cmap'] = 'viridis' print('Python version:\n{}\n'.format(sys.version)) print('Numpy version:\t\t{}'.format(np.__version__)) print('matplotlib version:\t{}'.format(matplotlib.__version__)) print('Scipy version:\t\t{}'.format(scipy.__version__))  Populating the interactive namespace from numpy and matplotlib Python version: 3.7.0 (default, Aug 17 2018, 19:20:07) [GCC 5.4.0 20160609] Numpy version: 1.16.1 matplotlib version: 3.0.2 Scipy version: 1.2.1  ## A Mathematical Model for Camera Noise¶ One of the best descriptions of camera noise that I have ever found may be the EMVA 1288 Standard. This document details a standard set of models and procedures to characterize CMOS and CCD cameras and light sensors. From its website: EMVA launched the initiative to define a unified method to measure, compute and present specification parameters for cameras and image sensors used for machine vision applications... [The EMVA Standard] creates transparency by defining reliable and exact measurement procedures as well as data presentation guidelines and makes the comparison of cameras and image sensors much easier. In particular, chapters 2 and 3 of the Standard provide a very clear and concise description the mathematical model for CCD/CMOS camera noise. Below, I have adapted the image of the mathematical model presented at the beginning of chapter 2. In this model, the camera/sensor is a single pixel that takes an input (a number of photons) and transforms this number to an output (a digital value in analog-to-digital units, or ADU). In performing this transformation, various sources of noise are added to the signal so that, given a camera's output in ADU, we can only make probabilisitic inferences about the actual number of photons impinging upon it. There are also a few assumptions in this model that, when taken together, constitute what's called an ideal image sensor. They are: 1. the numer of photons collected by the pixel depends on the product of irradiance$ E \, \left[ W / m^2 \right] $and the exposure time$ t_{exp} \, \left[ s \right] $; 2. the sensor is linear, i.e. the digital signal$ y $increases linearly with the number of photons received; 3. all noise sources are constant in time and space; 4. only the total quantum efficiency of the camera is dependent on the wavelength of the incident irradiation; 5. and only the dark current depends on the temperature. From these five assumptions, the laws of quantum mechanics, and the laws of probability, expressions for the mean output,$ \mu_y $, the variance of the output$ \sigma_y^2 $, and the signal-to-noise ratio ($SNR $) may be derived. \begin{equation*} \mu_y = K \mu_d + K \eta \mu_p \\ \sigma_y^2 = K^2 \sigma_d^2 + K \left( \mu_y - K \mu_d \right) \\ SNR = \frac{\eta \mu_p}{\sqrt{\sigma_d^2 + \sigma_q^2/K^2 + \eta \mu_p}} \end{equation*} In these expressions,$\mu$and$\sigma^2$represent the mean and variance of the number of photons hitting the camera ($p$), the dark noise ($d$), and the output signal in ADU's ($y$). The number of electrons$ \mu_e $generated by$\mu_p$photons hitting the active area of the sensor is obtained from the expression for the quantum efficiency$\eta$, an engineered property of the camera that in general depends on the wavelength. \begin{equation*} \eta \left( \lambda \right) = \frac{\mu_e}{\mu_p} \end{equation*} The sensitivity of the camera$K \, \left[ ADU / e^- \right] $represents the amplification of the voltage in the pixel from the photoelectrons and is also a property of the camera. Finally,$ \sigma_q^2 $represents the noise introduced by digitzing the continous voltage signal into a digital one. The EMVA 1288 Standard explains how to derive these expressions from the assumptions and known physical laws, so I will not go into their derivations in this post. Instead, I will focus on explaining how we can use this model to simulate the effects of camera noise in our holograms. ## From Model to Simulation¶ The goal of the simulation will be to take a simulated hologram as input and convert it into an image that might be captured by a digital camera. This means that the final image should contain noise that is realistic and follows the rules of the model. The model will depend on five free parameters that vary from camera-to-camera. They are: 1. the total quantum efficiency$ \eta $; 2. the read noise variance$ \sigma_{r}^2 $(or its standard deviation); 3. the dark current$ \mu_I $; 4. the sensitivity$K$; 5. and the bit-depth of the camera$k$. The dark noise$ \sigma_d^2 $is actually comprised of two separate noise sources, i.e. the read noise$ \sigma_r^2 $and the dark current$ \mu_I $. Because the noise sources are independent, we can write \begin{equation*} \sigma_d^2 = \sigma_r^2 + \sigma_I^2 \\ \sigma_d^2 = \sigma_r^2 + \mu_I t_{exp} \end{equation*} where the last step relies on the fact that the generation of thermal electrons is a Poisson process whose mean is equal to its variance. The units of$\mu_I$are$e^- / s $and values for$ \mu_I $are often provided on camera spec. sheets. Likewise, the read noise$\sigma_r^2$is also provided on spec. sheets, although in my experience the units are likely to be in root-mean-square electrons or median electrons and not electrons-squared. Other than the inputs, we do not need to provide values for the other numbers in the model because they are related to the free parameters by various physical and mathematical laws. Finally, let's ignore spatial noise sources in these simulations because it's difficult to characterize them with a single number. Spatial noise is a variation in the free parameters of the camera from pixel to pixel. An example of a common type of spatial noise is photon response non-uniformity and is manifest in a sensitivity$ K $that varies between pixels. Ignoring spatial noise in the simulations simply means that values for the read noise, dark current, quantum efficiency, and sensitivty are the same for all pixels. ### Step 0: Convert the electric field to photons¶ Before doing anything, we need to take the electric field from our Fourier optics simulations and convert it to units of photons. If it isn't clear how you would first get an electric field, you can refer to my previous post on calculating the hologram of a thin, circular phase-only object. Typically, the calcuation of the electric field will follow from the laws of diffraction and serve as an input for the camera model. To get the number of photons, we first compute the irradiance of the field using the magnitude of the time-averaged Poynting vector of a linearly-polarzed electromagnetic wave in free space, which is \begin{equation*} E \left(x, y \right) = \frac{1}{2Z_o} \left| U\left(x, y \right) \right|^2 \end{equation*} Here,$E \left( x, y \right) $is the irradiance at point$ \left( x, y \right) $,$U \left( x, y \right) $is the scalar electric field at the same point, and$Z_0 = 377 \, \Omega $is the impedance of free space. We would change the value for the impedance if we were imaging in a medium other than vacuum. The units of the field are$ V / m $which, when squared and divided by the units of the impedance (Ohms), gives units of power per area, or$ W / m^2 . It's also worth mentioning that we are implicitly assuming the field varies smoothly on the length scale of a pixel. This is why we can use the expression for the Poynting vector of a plane wave. The mean number of photons is obtained from the irradiance by the expression \begin{align*} \mu_p &= \frac{\lambda A}{hc}Et_{exp} \\ &= \frac{\lambda A}{2hcZ_0} \left| U \right|^2 t_{exp} \end{align*} where A $is the pixel's area and$ \frac{hc}{\lambda} $is the energy per photon in units of Joules, with$hc = 2 \times 10^{-25} \, J \cdot m $. This step is a bit cumbersome, and in the rest of what follows I will skip this step and will use a set number of photons directly as the input to the simulations, rather than a scalar field. ### Step 1: Compute the photon shot noise¶ For the sake of simplicity, let's start by assuming that we have a camera with$ 256 \times 256 $pixels and a mean incident photon flux of 500 photons on each pixel. This would produce an image that looks like this: In [2]: num_photons = 500 num_pixels = 256 mu_p = num_photons * np.ones((num_pixels, num_pixels)) fig, ax = plt.subplots() img = ax.imshow(mu_p, vmin=400, vmax=600) ax.set_xticks([]) ax.set_yticks([]) ax.set_title('No noise') cb = plt.colorbar(img) cb.set_label('Photons') plt.show()  Photon shot noise arises from the fact that the incident number of photons is not deterministic but rather a random process whose statistics are Poissonian. In a Poisson process, the variance of the noise$ \sigma_p^2 $is equal to the mean number of photons$ \mu_p $. Poisson random numbers are easy to generate with NumPy. First, we set a seed so that we can reproducibly generate the same random numbers each time and initialize a RandomState instance with it. Using this RandomState instance, we call the poisson method with a mean of num_photons and a size (num_pixels, num_pixels). Finally, we plot the image and compare it to the one where no shot noise is present. In [3]: seed = 42 rs = np.random.RandomState(seed) shot_noise = rs.poisson(num_photons, (num_pixels, num_pixels)) fig, (ax0, ax1) = plt.subplots(ncols=2) img0 = ax0.imshow(mu_p, vmin=400, vmax=600) ax0.set_xticks([]) ax0.set_yticks([]) ax0.set_title('No shot noise') divider = make_axes_locatable(ax0) cax = divider.append_axes("right", size="5%", pad=0.05) cb0 = plt.colorbar(img0, cax=cax) cb0.set_ticks([]) img1 = ax1.imshow(shot_noise, vmin=400, vmax=600) ax1.set_xticks([]) ax1.set_yticks([]) ax1.set_title('Shot noise') divider = make_axes_locatable(ax1) cax = divider.append_axes("right", size="5%", pad=0.05) cb1 = plt.colorbar(img1, cax=cax) cb1.set_label('Photons') plt.show()  In [4]: # It's also interesting to look at the distribution of photons hitting each pixel. plt.hist(shot_noise.ravel(), bins=np.arange(350, 650)) plt.xlabel('Number of photons per pixel') plt.ylabel('Frequency') plt.show()  ### Step 2: Compute the number of photoelectrons¶ At this point we're going to need some numbers for our camera. For this example, I chose a camera using the popular Sony IMX264 CMOS chip, the FLIR Chamleon 3 (part number CM3-U3-50S5M-CS). Here are some of the key specs for our modeling: Spec Value Quantum efficiency (at 525 nm) 0.69 Sensitivity 5.88 ADU / e- Temporal dark noise 2.29 e- Pixel size 3.45 microns Analog-to-digital converter (ADC) 12-bit Assuming our light has a wavelength of 525 nm, then the number of photoelectrons is simply the product of the quantum efficiency with the realization of the field. In [5]: quantum_efficiency = 0.69 # Round the result to ensure that we have a discrete number of electrons electrons = np.round(quantum_efficiency * shot_noise) fig, (ax0, ax1) = plt.subplots(ncols=2) img0 = ax0.imshow(shot_noise, vmin=200, vmax=600) ax0.set_xticks([]) ax0.set_yticks([]) ax0.set_title('Photons') divider = make_axes_locatable(ax0) cax = divider.append_axes("right", size="5%", pad=0.05) cb0 = plt.colorbar(img0, cax=cax) cb0.set_ticks([]) img1 = ax1.imshow(electrons, vmin=200, vmax=600) ax1.set_xticks([]) ax1.set_yticks([]) ax1.set_title('Electrons') divider = make_axes_locatable(ax1) cax = divider.append_axes("right", size="5%", pad=0.05) cb = plt.colorbar(img1, cax=cax) plt.show()  ### Step 3: Simulate read noise and dark current¶ Following the schematic of the camera model above, we see that we next need to add the dark noise. Dark noise (not to be confused with dark current) refers to the noise in the pixels when there is no light on the camera. Typically we deal with two sources of dark noise: readout (or just "read") noise and dark current. The camera specs in our example only provide us with the total dark noise, which is not surprising since dark current is not very significant in microscopy or machine vision. (It is however significant in astronomy because of the very long exposure times of several seconds or more, which allows appreciable dark current electrons to accumulate during the exposure.) To the best of my knowledge, when dark noise is primarily read noise we may well model it as a Gaussian distribution whose standard deviation is equivalent to the dark noise spec of the camera. This modeling approach is taken, for example, in the 2016 SMLMS Challenge, a community-driven competition to identify the best reconstruction algorithms for single molecule localization microscopy. Please note that the noise model employed in the challenge was for an electron multiplying CCD (EMCCD), so you may find that it differs slightly from what I am discussing here. In [6]: dark_noise = 2.29 # electrons electrons_out = np.round(rs.normal(scale=dark_noise, size=electrons.shape) + electrons) fig, (ax0, ax1) = plt.subplots(ncols=2) img0 = ax0.imshow(electrons, vmin=250, vmax=450) ax0.set_xticks([]) ax0.set_yticks([]) ax0.set_title('Electrons In') divider = make_axes_locatable(ax0) cax = divider.append_axes("right", size="5%", pad=0.05) cb0 = plt.colorbar(img0, cax=cax) cb0.set_ticks([]) img1 = ax1.imshow(electrons_out, vmin=250, vmax=450) ax1.set_xticks([]) ax1.set_yticks([]) ax1.set_title('Electrons Out') divider = make_axes_locatable(ax1) cax = divider.append_axes("right", size="5%", pad=0.05) cb = plt.colorbar(img1, cax=cax) cb.set_label('Electrons') plt.show()  In [7]: # Plot the difference between the two fig, ax = plt.subplots() img = ax.imshow(electrons - electrons_out, vmin=-10, vmax=10) ax.set_xticks([]) ax.set_yticks([]) ax.set_title('Difference') cb = plt.colorbar(img) cb.set_label('Electrons') plt.show()  ### Step 4: Convert from$ e^- $to ADU¶ Now we need to convert the value of each pixel from electrons to ADU, or analog-to-digital units. ADU's are the units of grey scale that are output by monochrome cameras. To do this, we multiply the number of electrons after the addition of read noise by the sensitivity. We also need to ensure that the final ADU count is discrete and to set the maximum upper value of ADU's to the$ 2^k - 1 $where$ k \$ is the camera's bit-depth. The latter operation ensures that saturation of the pixels is correctly modeled.

In [8]:
sensitivity = 5.88 # ADU/e-
bitdepth    = 12