Merge branch 'master' of https://github.com/rjdmoore/fictrac into shmem

README.md

@@ -1,6 +1,4 @@
-<div align="left">
-  <img src="http://rjdmoore.net/fictrac/header_text.jpg"><br><br>
-</div>
+![FicTrac: The webcam-based method for tracking spherical motion and generating fictive animal paths](https://user-images.githubusercontent.com/3844483/110451048-176e9300-80c4-11eb-8e1e-e96545d7d2ed.jpg)
 
 **FicTrac** is an open-source software library for reconstructing the fictive path of an animal walking on a patterned sphere. The software is fast, flexible, easy to use, and simplifies the setup of closed-loop tracking experiments.
 
@@ -53,7 +51,7 @@ The FicTrac source code can be built for both Windows and Linux (e.g. Ubuntu) op
     2. Linux only:
         1. Run the following from terminal to install necessary build tools and dependencies:
         ```
-        [Linux] sudo apt-get install gcc g++ git cmake curl unzip tar yasm pkg-config libgtk2.0-dev libavformat-dev libavcodec-dev libavresample-dev libswscale-dev libopencv-dev
+        sudo apt-get install gcc g++ git cmake curl unzip tar yasm pkg-config libgtk2.0-dev libavformat-dev libavcodec-dev libavresample-dev libswscale-dev libopencv-dev
         ```
     3. (Windows and Linux) Clone or download the [Vcpkg](https://github.com/Microsoft/vcpkg) repository and then follow the guide to install (make sure to perform the bootstrap and integration steps).
     4. Using Vcpkg, install remaining dependencies:
@@ -125,7 +123,7 @@ Before running FicTrac, you may configure your camera (frame rate, resolution, e
   <summary>Basler Pylon SDK</summary>
 
 1. Download and install the latest [Pylon SDK](https://www.baslerweb.com/en/products/software/basler-pylon-camera-software-suite/).
-2. When preparing the build files for FicTrac using Cmake, you will need to specify to use Pylon using the switch `-D PGR_USB3=ON` and depending on where you installed the SDK, you may also need to provide the SDK directory path using the switch `-D BASLER_DIR=...`. For example, for a Windows installation you would replace step 3 above with (replacing <vcpkg_root> with the path to your vcpkg root directory):
+2. When preparing the build files for FicTrac using Cmake, you will need to specify to use Pylon using the switch `-D BASLER_USB3=ON` and depending on where you installed the SDK, you may also need to provide the SDK directory path using the switch `-D BASLER_DIR=...`. For example, for a Windows installation you would replace step 3 above with (replacing <vcpkg_root> with the path to your vcpkg root directory):
 ```
 cmake -A x64 -D CMAKE_TOOLCHAIN_FILE=<vcpkg root>/scripts/buildsystems/vcpkg.cmake -D BASLER_USB3=ON -D BASLER_DIR="C:\path\to\Pylon" ..
 ```

azure-pipelines.yml

@@ -5,8 +5,8 @@
 # https://docs.microsoft.com/en-us/azure/devops/pipelines/build/triggers?view=azure-devops&tabs=yaml
 
 trigger:
-#- master
-- develop
+- master
+#- develop
 
 # We can run multiple jobs in parallel.
 # see https://docs.microsoft.com/en-us/azure/devops/pipelines/process/phases

doc/params.md

@@ -24,7 +24,7 @@ In the table below, the various possible parameters are listed. If nothing is li
 | thr_ratio  | float      | 1.25          | (0,inf)     | Only if you need to | Adjusts the adaptive thresholding of the input image. Values > 1 will favour foreground regions (more white in thresholded image) and values < 1 will favour background regions (more black in thresholded image). |
 | thr_win_pc | float      | 0.2           | \[0,1]      | Only if you need to | Adjusts the size of the neighbourhood window to use for adaptive thresholding of the input image, specified as a percentage of the width of the tracking window. Larger values avoid over-segmentation, whilst smaller values make segmentation more robust to illumination gradients on the trackball. |
 | vid_codec  | string     | h264          | [h264,xvid,mpg4,mjpg,raw] | Only if you need to | Specifies the video codec to use when writing output videos (see `save_raw` and `save_debug`). |
-| sphere_map_fn | string  |               |             | Only if you need to | If specified, FicTrac will attempt to load a previously generated sphere surface map from this filename. |
+| sphere_map_fn | string  |               |             | Only if you need to | If specified, FicTrac will attempt to load a previously generated sphere surface map from this filename. Note that if you set this option, you should probably also set `opt_do_global` otherwise FicTrac may not find the initial sphere attitude. |
 |            |            |               |             |                     |             |
 | opt_max_evals | int     | 50            | (0,inf)     | Probably not        | Specifies the maximum number of minimisation iterations to perform each frame. Smaller values may improve tracking frame rate at the risk of finding sub-optimal matches. Number of optimisation iterations is printed to screen during tracking (its=...). |
 | opt_bound  | float      | 0.35          | (0,inf)     | Probably not        | Specifies the optimisation search range in radians. Larger values will facilitate more track ball rotation per frame, but result in slower tracking and also possibly lead to false matches. |

include/typesvars.h

@@ -15,8 +15,3 @@ const CmReal CM_PI   = 3.14159265358979323846;
 const CmReal CM_PI_2 = 1.57079632679489661923;
 const CmReal CM_R2D  = 180.0 / CM_PI;
 const CmReal CM_D2R  = CM_PI / 180.0;
-
-//enum THR_MODE {
-//    ADAPT,
-//    NORM_PRIORS
-//};

scripts/socket_client.py

@@ -1,58 +1,75 @@
 #!/usr/bin/env python3
 
 import socket
+import select
 
 HOST = '127.0.0.1'  # The (receiving) host IP address (sock_host)
 PORT = ????         # The (receiving) host port (sock_port)
 
+# TCP
 # Open the connection (ctrl-c / ctrl-break to quit)
-with socket.socket(socket.AF_INET, socket.SOCK_DGRAM) as sock:		# UDP
-#with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:	# TCP
-    sock.bind((HOST, PORT))		# UDP
-#    sock.connect((HOST, PORT))	# TCP
-
-    data = ""
+#with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:
+#    sock.connect((HOST, PORT))
+
+# UDP
+# Open the connection (ctrl-c / ctrl-break to quit)
+with socket.socket(socket.AF_INET, socket.SOCK_DGRAM) as sock:
+    sock.bind((HOST, PORT))
+    sock.setblocking(0)
 
     # Keep receiving data until FicTrac closes
+    data = ""
+    timeout_in_seconds = 1
     while True:
-        # Receive one data frame
-        new_data = sock.recv(1024)
-        if not new_data:
-            break
-
-        # Decode received data
-        data += new_data.decode('UTF-8')
-
-        # Find the first frame of data
-        endline = data.find("\n")
-        line = data[:endline]       # copy first frame
-        data = data[endline+1:]     # delete first frame
-
-        # Tokenise
-        toks = line.split(", ")
-
-		# Check that we have sensible tokens
-        if ((len(toks) < 24) | (toks[0] != "FT")):
-            print('Bad read')
-            continue
-
-        # Extract FicTrac variables
-        # (see https://github.com/rjdmoore/fictrac/blob/master/doc/data_header.txt for descriptions)
-        cnt = int(toks[1])
-        dr_cam = [float(toks[2]), float(toks[3]), float(toks[4])]
-        err = float(toks[5])
-        dr_lab = [float(toks[6]), float(toks[7]), float(toks[8])]
-        r_cam = [float(toks[9]), float(toks[10]), float(toks[11])]
-        r_lab = [float(toks[12]), float(toks[13]), float(toks[14])]
-        posx = float(toks[15])
-        posy = float(toks[16])
-        heading = float(toks[17])
-        step_dir = float(toks[18])
-        step_mag = float(toks[19])
-        intx = float(toks[20])
-        inty = float(toks[21])
-        ts = float(toks[22])
-        seq = int(toks[23])
+        # Check to see whether there is data waiting
+        ready = select.select([sock], [], [], timeout_in_seconds)
+
+        # Only try to receive data if there is data waiting
+        if ready[0]:
+            # Receive one data frame
+            new_data = sock.recv(1024)
+
+            # Uh oh?
+            if not new_data:
+                break
+
+            # Decode received data
+            data += new_data.decode('UTF-8')
+
+            # Find the first frame of data
+            endline = data.find("\n")
+            line = data[:endline]       # copy first frame
+            data = data[endline+1:]     # delete first frame
+
+            # Tokenise
+            toks = line.split(", ")
+
+            # Check that we have sensible tokens
+            if ((len(toks) < 24) | (toks[0] != "FT")):
+                print('Bad read')
+                continue
+
+            # Extract FicTrac variables
+            # (see https://github.com/rjdmoore/fictrac/blob/master/doc/data_header.txt for descriptions)
+            cnt = int(toks[1])
+            dr_cam = [float(toks[2]), float(toks[3]), float(toks[4])]
+            err = float(toks[5])
+            dr_lab = [float(toks[6]), float(toks[7]), float(toks[8])]
+            r_cam = [float(toks[9]), float(toks[10]), float(toks[11])]
+            r_lab = [float(toks[12]), float(toks[13]), float(toks[14])]
+            posx = float(toks[15])
+            posy = float(toks[16])
+            heading = float(toks[17])
+            step_dir = float(toks[18])
+            step_mag = float(toks[19])
+            intx = float(toks[20])
+            inty = float(toks[21])
+            ts = float(toks[22])
+            seq = int(toks[23])
+
+            # Do something ...
+            print(cnt)
 
-        # Do something ...
-        print(cnt)
+        else:
+            # Didn't find any data - try again
+            print('retrying...')

src/Trackball.cpp

@@ -864,12 +864,15 @@ void Trackball::updateSphere()
             uint8_t& map = _sphere_map.data[py * _sphere_map.step + px];
 
             // update map tile
-            if (map == 128) {
+            if ((map == 0) || (map == 255)) {
+                // map tile frozen
+                good++;
+            } else if (map == 128) {
                 // map tile previously unseen
                 map = (proi[j] == 255) ? (128 + SPHERE_MAP_FIRST_HIT_BONUS) : (128 - SPHERE_MAP_FIRST_HIT_BONUS);
             } else {
                 good++;
-                map = min(max((proi[j] == 255) ? (int(map) + 1) : (int(map) - 1), 0), 255);
+                map = (proi[j] == 255) ? (map + 1) : (map - 1);
             }
 
             // display