Apply calibration to Jungfrau raw data (#216)

- Added function to read calibration file
- Multi threaded pedestal subtraction and application of the calibration

python/tests/test_calibration.py

@@ -0,0 +1,43 @@
+import pytest 
+import numpy as np
+from aare import apply_calibration
+
+def test_apply_calibration_small_data():
+    # The raw data consists of 10 4x5 images
+    raw = np.zeros((10, 4, 5), dtype=np.uint16)
+
+    # We need a pedestal for each gain, so 3 
+    pedestal = np.zeros((3, 4, 5), dtype=np.float32)
+
+    # And the same for calibration
+    calibration = np.ones((3, 4, 5), dtype=np.float32)
+
+    # Set the known values, probing one pixel in each gain
+    raw[0, 0, 0] = 100 #ADC value of 100, gain 0
+    pedestal[0, 0, 0] = 10
+    calibration[0, 0, 0] = 43.7
+
+    raw[2, 3, 3] = (1<<14) + 1000 #ADC value of 1000, gain 1
+    pedestal[1, 3, 3] = 500
+    calibration[1, 3, 3] = 2.0
+
+    raw[1,1,4] = (3<<14) + 857 #ADC value of 857, gain 2
+    pedestal[2,1,4] = 100
+    calibration[2,1,4] = 3.0
+
+    
+
+    data = apply_calibration(raw, pd = pedestal, cal = calibration)
+
+
+    # The formula that is applied is:
+    # calibrated = (raw - pedestal) / calibration
+    assert data.shape == (10, 4, 5)
+    assert data[0, 0, 0] == (100 - 10) / 43.7
+    assert data[2, 3, 3] ==  (1000 - 500) / 2.0
+    assert data[1, 1, 4] == (857 - 100) / 3.0
+
+    # Other pixels should be zero
+    assert data[2,2,2] == 0
+    assert data[0,1,1] == 0
+    assert data[1,3,0] == 0