From aa23d66bd23310be170fd20fbffb3230824847ae Mon Sep 17 00:00:00 2001
From: tpollina <thibaut.pollina@gmail.com>
Date: Fri, 13 Dec 2019 14:51:50 -0800
Subject: [PATCH] Add files via upload

---
 scripts/README.md | 52 +++++++++++++++++++++++++----------------------
 scripts/image.py  | 14 +++++++------
 scripts/killer.sh |  2 +-
 3 files changed, 37 insertions(+), 31 deletions(-)

diff --git a/scripts/README.md b/scripts/README.md
index 311fcc6..3ea4699 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -21,6 +21,34 @@ Example:
 
     python3.7 $HOME/PlanktonScope/scripts/pump.py 1 10 suck
     
+_________________
+### Image
+##### image.py `in_path` `sample_project` `sample_id` `acq_id` `volume` `flowrate`
+
+- `in_path` : **string** - directory to store acquisitions **the path has to end with /**
+- `sample_project` : **string**
+- `sample_id` : **string**
+- `acq_id` : **string**
+- `volume` : **integer**
+- `flowrate` : **float**
+
+Example:
+
+    python3.7 $HOME/PlanktonScope/scripts/image.py $HOME/PlanktonScope/Acquisitions/ tara_pacific station_125 exp_1 24 3.2
+    
+
+_________________
+
+### Light
+##### light.py `state`
+
+- `state` : **string**
+
+Example:
+
+    python3.7 $HOME/PlanktonScope/scripts/light.py on
+
+
 _________________
 ### Killing Focus or Pump event
 ##### killer.sh `event_to_kill.py`
@@ -32,20 +60,6 @@ Example:
 
     bash $HOME/PlanktonScope/scripts/killer.sh pump.py
     
-_________________
-### Image
-##### image.py `sample_project` `sample_id` `acq_id` `volume` `flowrate`
-
--`sample_project` : **string**
-- `sample_id` : **string**
-- `acq_id` : **string**
-- `volume` : **integer**
-- `flowrate` : **float**
-
-Example:
-
-    python3.7 $HOME/PlanktonScope/scripts/pump.py tara_pacific station_125 exp_1 24 3.2
-    
 _________________
 ### Kill Image
 ##### kill_image.sh image.py `sample_project` `sample_id` `acq_id`
@@ -58,13 +72,3 @@ Example:
 
     bash $HOME/PlanktonScope/scripts/killer.sh image.py tara_pacific station_125 exp_1
     
-_________________
-
-### Light
-##### light.py `state`
-
-- `state` : **string**
-
-Example:
-
-    python3.7 $HOME/PlanktonScope/scripts/light.py on
diff --git a/scripts/image.py b/scripts/image.py
index 94367d5..f538864 100644
--- a/scripts/image.py
+++ b/scripts/image.py
@@ -11,20 +11,22 @@ from datetime import datetime, timedelta
 import os
 import sys
 
+in_path = str(sys.argv[1])
+
 #[t] : ex:tara_pacific
-sample_project = str(sys.argv[1])
+sample_project = str(sys.argv[2])
 
 #[t] : unique identifier
-sample_id = str(sys.argv[2])
+sample_id = str(sys.argv[3])
 
 #[t] : unique identifier
-acq_id = str(sys.argv[3])
+acq_id = str(sys.argv[4])
 
 #[i] : ex:24ml
-volume = int(sys.argv[4])
+volume = int(sys.argv[5])
 
 #[f] : ex:3.2ml/min
-flowrate = float(sys.argv[5])
+flowrate = float(sys.argv[6])
 
 warm_up_duration=3
 
@@ -34,7 +36,7 @@ max_fps = 0.7
 
 nb_frame = int(duration/max_fps)
 
-path= "/home/pi/"+sample_project+"/"+sample_id+"/"+acq_id+"/"
+path= in_path+sample_project+"/"+sample_id+"/"+acq_id+"/"
     
 if not os.path.exists(path):
     os.makedirs(path)
diff --git a/scripts/killer.sh b/scripts/killer.sh
index 5f2d4fb..99fee90 100644
--- a/scripts/killer.sh
+++ b/scripts/killer.sh
@@ -3,6 +3,6 @@
 
 scrip_name=$1
 
-kill -9 `ps ax | grep "$scrip_name" | head -1 | awk '{print $1}'
+kill -9 `ps ax | grep "$scrip_name" | head -1 | awk '{print $1}'`
 
 python3.7 $HOME/PlanktonScope/scripts/recover.py