Kubke Lab:Research/ABR/Notebook/2013/11/05: Difference between revisions
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=General Entries= | =General Entries= | ||
* | * Skyped Andy vs Fabiana - trying to get an idea of the structure of the raw data files and make sure that the extracted text files are ok. Seems everything is ok, header log file contains all header info (albeit in a strange format). Different version files have different info, eg, some versions have the SD of the data others don't. Need to consider when extracting/analysing that the number of columns etc are going to vary from file to file. | ||
=Personal Entries= | =Personal Entries= | ||
==Fabiana== | ==Fabiana== | ||
===Reading the binary files === | |||
*trying to open the actual .ABR files - getting nowhere. Noticed the log files that were extracted dont have the info I need and need to see what info is in the actual data files. | *trying to open the actual .ABR files - getting nowhere. Noticed the log files that were extracted dont have the info I need and need to see what info is in the actual data files. | ||
Andy says it is an intel file - over skype trying to figure out the structure so we can read it - extracting info from | Andy says it is an intel file - over skype trying to figure out the structure so we can read it - extracting info from | ||
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</pre> | </pre> | ||
=== Extracting info from log file=== | |||
== Extracting info from log file== | |||
# From file 2013-11-050b-MFK.Rmd (in sandbox) | # From file 2013-11-050b-MFK.Rmd (in sandbox) | ||
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==Andy== | ==Andy== | ||
===ABR.H header file=== | |||
Following file is from the ABR.H header file that was used for the original files. | Following file is from the ABR.H header file that was used for the original files. | ||
Revision as of 03:05, 5 November 2013
 Hearing development in barn owls
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General Entries
Personal EntriesFabianaReading the binary files
Andy says it is an intel file - over skype trying to figure out the structure so we can read it - extracting info from abr.h and abr_4_mac.c According to andy need to Read the first 1128 bytes then read the next 1000 2-byte int skip 52 read next 1000 points, and so on rawData = file("189L0A.ABR", "rb")
a <- readBin(rawData,integer(),file.info("189L0A.ABR")$size,size = 2)
#size2 says integer is 2 bytes
close(rawData)
plot(a)
plot(a, ylim = c(-500,500))
#at the begining there is 564points that correspond to the header
#If I clean up the header
plot(a[562:2565], type="line")
str(a)
b<-seq(1,length(a), 2)
c<-seq(2,length(a),2)
plot(a[b])
plot(a[c])
aclean<-a[562:2565]
head(aclean)
head(aclean[b])
head(aclean[c])
plot(aclean[b], xlim=c(0,1000))
plot(aclean[c], xlim=c(0,1000))
Extracting info from log file
<html> <body> <h1>Trying to extract info from the log files</h1> <p>Filename: “419L76.ABR.log”</p> <p>This is what the notepad shows:</p> <p>Owl Date Time Clock_kHz n_reps freq version 419 05/30/93 14:22:22 50 25 5000 5.30 Comment line: Luxman -43 Auxkl B norm 100 valium used Channel 0 data, only</p> <p>delay 0 -160 -100 -180 -140</p> <p>I want to extract [1:7] -> headers [8:14] -> info rest -> comment line tail -> delays</p> <pre><code class="r">logfile <- read.delim2("419L76.ABR.log", sep = "\t", header = T) head(logfile) </code></pre> <pre><code>## Owl
</code></pre> <pre><code class="r">str(logfile) </code></pre> <pre><code>## 'data.frame': 9 obs. of 7 variables:
</code></pre> <p>I get a funny looking table</p> <pre><code class="r">loghead <- read.table("419L76.ABR.log", header = T, sep = "\t", nrows = 1, skip = 0) </code></pre> <p>This gets me the descriptor - still need to get the other rows</p> <pre><code class="r">loghead <- read.table("419L76.ABR.log", header = T, sep = "\t", nrows = 1, skip = 0) loganaesth <- read.table("419L76.ABR.log", sep = "\t", nrows = 1, skip = 2) logtail <- read.table("419L76.ABR.log", sep = "\t", col.names = "Owl", nrows = 20, skip = 3) print(loghead) </code></pre> <pre><code>## Owl Date Time Clock_kHz n_reps freq version
</code></pre> <pre><code class="r">print(loganaesth) </code></pre> <pre><code>## V1 V2
</code></pre> <pre><code class="r">print(logtail) </code></pre> <pre><code>## Owl
</code></pre> <p>Data file 419L76.ABR.txt read.table gives me an error that there is a mismatch betweeen columns and column names - but read.delim2 seems to solve the problem, although it creates a last column x with NAs (which is probably what is generating the problem in hte first place.)</p> <pre><code class="r">data <- read.delim2("419L76.ABR.txt", sep = "\t", header = T) head(data) </code></pre> <pre><code>## msec left right spont bin.0 bin.1 bin.2 bin.3 bin.4 sdev_l sdev_r
</code></pre> <p>returns 5 columns of bin.[0:4] - which probably correspond to the 5 delays in the log file. </p> </body> </html> AndyABR.H header fileFollowing file is from the ABR.H header file that was used for the original files. File layout is probably: <Master_Header><Sub_Structure><1000 2-byte INT><Sub_Structure><1000 2-byte INT> ... This structure needs to be confirmed.
typedef struct {
short freq; /* frequency in Hz */
short amp; /* amplitude in D/A units */
short dur; /* duration in clock ticks */
short rise_fall; /* rise_fall in clock ticks */
} SIGNAL; // 8 bytes
typedef struct {
SIGNAL carrier;
SIGNAL envelope;
} STIMULUS;
typedef struct {
short left_delay; /* microseconds to left onset */
short right_delay; /* microseconds to right onset */
short rep_shorterval; /* interval in millseconds */
} TIMING; //6 bytes
typedef struct {
short clock; /* clock frequency in kHz */
short max_size; /* maximum size of each array */
short channels; /* 1 for carrier only, 2 for carrier & envelope */
} DA_INFO; //6 bytes
typedef struct {
short clock; /* in kHz */
short size; /* number of elements (per channel) */
short channels; /* number of channels */
short avg_reps; /* number of reps making up the average */
} AD_INFO; //8 bytes
typedef struct {
char date[12];
char time[12];
char owl_id[12];
char exp_id[12];
char comments[80];
short depth;
short version;
char side;
short num_chan;
short num_tests;
short gain;
char extra_room[1024-(12+12+12+12+80+2+2+1+2+2+2)];/* Add two more to correct CHAR */
// char extra_room[1024-(12+12+12+12+80+2+2+1)];/* Add two more to correct CHAR */
} HEADER_INFO, EXPERIMENT_HEADER; // Bytes 1024
typedef struct /**** THE MASTER STRUCTURE ****/ {
HEADER_INFO header; //1024
STIMULUS left; // 16
STIMULUS right; // 16
TIMING delay; // 6
DA_INFO output; // 6
AD_INFO input; // 8
} EXPERIMENT; // 1076 bytes
{
STIMULUS left; // 16
STIMULUS right; // 16
TIMING delay; // 6
DA_INFO output; // 6
AD_INFO input; // 8
} EXPERIMENT_INFO; // 52 bytes
Oris
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