joefutrelle

/**
 * Author: Joe Futrelle
 * License: CC0 - Free as in freedom
 */
/**
 * ATtiny85 direct digital synthesis
 * using MCP4725 12-bit I2C DAC
 * TWI is handled using Atmel's USI TWI implementation
 * which is provided as part of Application Note AVR310
 * http://www.atmel.com/Images/Atmel-2561-Using-the-USI-Module-as-a-I2C-Master_AP-Note_AVR310.pdf

joefutrelle

#include <avr/io.h>
#include <avr/interrupt.h>
#include <avr/wdt.h>
#include <avr/sleep.h>
#include <util/delay.h>

// cribbing from http://electronics.stackexchange.com/a/74850

void prevent_wdt_reset() {
  if(MCUSR & _BV(WDRF)){            // If a reset was caused by the Watchdog Timer...

joefutrelle

/* Name: main.c
 * Author: Joe Futrelle
 * License: CC0 - Free as in freedom
 */
/* Adafruit 4-digit alphanumeric backpack, I2C
 * Via USI_TWI_master from application note AVR310
 * http://www.atmel.com/Images/Atmel-2561-Using-the-USI-Module-as-a-I2C-Master_AP-Note_AVR310.pdf
 */
/* Datasheet for HT16K33
 * http://www.adafruit.com/datasheets/ht16K33v110.pdf

joefutrelle

joefutrelle

<namespace name="ifcb.utils">
  <rule name="reorg_products" include="src dest">
    <invoke rule="ifcb.files.find_data_dirs"/>
    <!-- directory=product root dir, product=product type -->
    <any>
      <test var="product" eq="blobs">
	<path var="src" match="${directory}/[0-9]*/[0-9]*/*_blobs_v2.zip"/>
	<match var="src" pattern=".*/((.*_blobs).*)" groups="product_filename pid"/>
	<invoke rule="ifcb.pid"/>
      </test>

joefutrelle

import os
import re
import time
from urllib2 import urlopen
import json

FEED_URL='http://ifcb-data.whoi.edu/mvco/feed.json'
DATA_DIR='/data'
FORMATS=('hdr','adc','roi')

joefutrelle

#include <Wire.h>

#define EEP_ADDR 0x50

void dump();

void setup()
{
  Wire.begin();        // join i2c bus (address optional for master)
  Serial.begin(9600);  // start serial for output

joefutrelle

#!/env/python
import sys
import os

import numpy as np
import pandas as pd

from pandas.io.parsers import read_csv

BASE_PATH='/media/F_DRIVE/FSM 2014'

joefutrelle

#!/env/python
import os
from glob import glob
from tifffile import TiffFile

BASE_DIR='{whatever}'

for tfpath in sorted(glob(os.path.join(BASE_DIR,'*.tif'))):
    tf = TiffFile(tfpath)
    tfn = os.path.basename(tfpath)

joefutrelle

from skimage.feature import peak_local_max
from skimage.filter import threshold_otsu
import scipy.ndimage as ndi

def count_bright(Y):
    t = threshold_otsu(Y)
    D = ndi.distance_transform_edt(Y > t)
    Pl = peak_local_max(D,indices=False)
    _, count = ndi.label(Pl)
    return count