GIT: Merge branch 'development'

.gitignore

@@ -108,6 +108,10 @@ firmware/mmc3_8chip_eth/vivado/*
 firmware/mmc3_8chip_multi_tx_eth/vivado/*
 !firmware/mmc3_8chip_multi_tx_eth/vivado/*.xpr
 
+# MMC3 8chip with multi TX SHIP firmware
+firmware/mmc3_8_chip_multi_tx_eth_SHIP/vivado/*
+!firmware/mmc3_8_chip_multi_tx_eth_SHIP/vivado/*.xpr
+
 # Simulation output
 firmware/mio/cosim/sim_build
 firmware/mio/cosim/sim_build.zip

.travis.yml

@@ -5,7 +5,6 @@ python:
 
 branches:
   only:
-    - master
     - development
 
 notifications:
@@ -38,13 +37,15 @@ install:
   - conda update --yes conda
   - conda update --yes --all
   - conda info -a
-  - conda create --yes -n test-environment python=$TRAVIS_PYTHON_VERSION bitarray cython ipython matplotlib mock nose numba numpy pyserial pytables pyyaml pyzmq scipy sphinx
+  - conda create --yes -n test-environment python=$TRAVIS_PYTHON_VERSION bitarray cython ipython matplotlib mock nose numba numpy pyqt pyserial pytables pyyaml pyzmq qtpy scipy
   - source activate test-environment
   - pip install progressbar-latest pyvisa pyvisa-py git+https://github.com/pyqtgraph/[email protected]
   - pip install pyusb
   - pip install pySiLibUSB
-  - if [ "$TRAVIS_BRANCH" == "master" ]; then pip install 'basil_daq>=2.4.9,<3.0.0' git+https://github.com/SiLab-Bonn/pyBAR_fei4_interpreter@development 'pixel_clusterizer>=3.1,<3.2'; fi
-  - if [ "$TRAVIS_BRANCH" == "development" ]; then pip install 'basil_daq>=2.4.9,<3.0.0' git+https://github.com/SiLab-Bonn/pyBAR_fei4_interpreter@development 'pixel_clusterizer>=3.1,<3.2'; fi
+  - pip install 'basil_daq>=2.4.12,<3.0.0'
+  #- pip install git+https://github.com/SiLab-Bonn/basil@development
+  - pip install git+https://github.com/SiLab-Bonn/pyBAR_fei4_interpreter@development
+  - pip install 'pixel_clusterizer>=3.1,<3.2'
   # Install pyBAR
   - python setup.py develop
 

MANIFEST.in

@@ -1,5 +1,6 @@
 include README.* VERSION LICENSE.txt requirements.txt
-include pybar/*.yaml pybar/*.bit
+include pybar/*.yaml
 recursive-include examples *
 recursive-include firmware *
 recursive-include pybar/config *
+recursive-include pybar/firmware *

README.md

@@ -1,5 +1,5 @@
 
-# pyBAR [![Code Status](https://landscape.io/github/SiLab-Bonn/pyBAR/master/landscape.svg?style=flat)](https://landscape.io/github/SiLab-Bonn/pyBAR/master) [![Build Status](https://travis-ci.org/SiLab-Bonn/pyBAR.svg?branch=master)](https://travis-ci.org/SiLab-Bonn/pyBAR) [![Build Status](https://ci.appveyor.com/api/projects/status/github/SiLab-Bonn/pyBAR?svg=true)](https://ci.appveyor.com/project/DavidLP/pybar-71xwl)
+# pyBAR [![Code Status](https://landscape.io/github/SiLab-Bonn/pyBAR/development/landscape.svg?style=flat)](https://landscape.io/github/SiLab-Bonn/pyBAR/development) [![Build Status](https://travis-ci.org/SiLab-Bonn/pyBAR.svg?branch=development)](https://travis-ci.org/SiLab-Bonn/pyBAR/branches) [![Build Status](https://ci.appveyor.com/api/projects/status/github/SiLab-Bonn/pyBAR?branch=development&svg=true)](https://ci.appveyor.com/project/laborleben/pybar-71xwl?branch=development)
 
 pyBAR - Bonn ATLAS Readout in Python
 
@@ -41,12 +41,12 @@ The following packages are required for pyBAR's core functionality:
 
 For full functionality, the following additional packages are required:
   ```
-  ipython mock nose pyqtgraph pyserial pyvisa pyvisa-py pyzmq sphinx vitables
+  ipython mock nose pyqtgraph pyserial pyvisa pyvisa-py pyzmq vitables
   ```
 
 Run the **following commands** to install the packages:
   ```
-  conda install python=2.7 bitarray contextlib2 cython ipython matplotlib mock nose numba numpy pyserial pytables pyyaml pyzmq scipy sphinx
+  conda install python=2.7 bitarray contextlib2 cython ipython matplotlib mock nose numba numpy pyqt pyserial pytables pyyaml pyzmq qtpy scipy
 
   pip install progressbar-latest pyvisa pyvisa-py git+https://github.com/pyqtgraph/[email protected]
   ```
@@ -56,9 +56,9 @@ On Windows, the `pywin32` package is required:
   conda install pywin32
   ```
 
-[Basil](https://github.com/SiLab-Bonn/basil) (>=2.4.9,<3.0.0) is required:
+[Basil](https://github.com/SiLab-Bonn/basil) (>=2.4.12,<3.0.0) is required:
   ```
-  pip install 'basil_daq>=2.4.9,<3.0.0'
+  pip install 'basil_daq>=2.4.12,<3.0.0'
   ```
 
 [pyBAR FEI4 Interpreter](https://github.com/SiLab-Bonn/pyBAR_fei4_interpreter) (>=1.3.0) is required:

VERSION

@@ -1 +1 @@
-3.0.2
+3.1.0.dev0

appveyor.yml

@@ -19,14 +19,15 @@ install:
   - conda update conda --yes
   - conda update --all --yes
   - conda info -a
-  - conda install --yes bitarray cython ipython matplotlib mock nose numba numpy pyserial pytables pyyaml pyzmq scipy sphinx
+  - conda install --yes bitarray cython ipython matplotlib mock nose numba numpy pyqt pyserial pytables pyyaml pyzmq qtpy scipy
   - conda install --yes pywin32
   - pip install progressbar-latest pyvisa pyvisa-py git+https://github.com/pyqtgraph/[email protected] #git+https://github.com/uvemas/ViTables@develop
   # test packages required for USB interface
   - pip install pyusb
   - pip install pySiLibUSB
   # pyBAR installation including additional specific packages
-  - pip install 'basil_daq>=2.4.9,<3.0.0'
+  - pip install 'basil_daq>=2.4.12,<3.0.0'
+  #- pip install git+https://github.com/SiLab-Bonn/basil@development
   - pip install git+https://github.com/SiLab-Bonn/pyBAR_fei4_interpreter@development
   - pip install 'pixel_clusterizer>=3.1,<3.2'
   - python.exe setup.py develop

examples/example_tdc/example_tdc.py

@@ -13,18 +13,17 @@
 
 from pybar.run_manager import RunManager  # importing run manager
 from pybar.scans.scan_iv import IVScan
-from pybar.scans.scan_init import InitScan
 from pybar.scans.test_register import RegisterTest
 from pybar.scans.scan_digital import DigitalScan
 from pybar.scans.scan_analog import AnalogScan
 from pybar.scans.tune_fei4 import Fei4Tuning
-from pybar.scans.tune_stuck_pixel import StuckPixelScan
+from pybar.scans.tune_stuck_pixel import StuckPixelTuning
 from pybar.scans.scan_threshold_fast import FastThresholdScan
 from pybar.scans.tune_noise_occupancy import NoiseOccupancyTuning
 from pybar.scans.calibrate_plsr_dac import PlsrDacScan
 from pybar.scans.calibrate_hit_or import HitOrCalibration
 from pybar.scans.scan_ext_trigger import ExtTriggerScan
-from pybar.fei4.register_utils import make_box_pixel_mask_from_col_row, parse_global_config
+from pybar.fei4.register_utils import make_box_pixel_mask_from_col_row
 import pybar.scans.analyze_source_scan_tdc_data as tdc_analysis
 
 
@@ -106,7 +105,7 @@ def plot_landau(source_scan_filename, tdc_hists, target_threshold, fit_range=(13
         plt.clf()
         plt.grid()
         x_fit_range = np.logical_and(charge > fit_range[0], charge < fit_range[1])
-        coeff, err = fit_landau_bootstrap(charge[x_fit_range], count[x_fit_range], p0 = (7000, np.std(charge[x_fit_range]), 150, np.amax(count[x_fit_range])), yerr=count_error[x_fit_range], n_iterations=100)
+        coeff, err = fit_landau_bootstrap(charge[x_fit_range], count[x_fit_range], p0=(7000, np.std(charge[x_fit_range]), 150, np.amax(count[x_fit_range])), yerr=count_error[x_fit_range], n_iterations=100)
         plt.bar(charge, count, width=charge[1] - charge[0], color='blue', label='data')
         plt.plot(charge[x_fit_range], landau.langau(charge[x_fit_range], *coeff), 'r-')
         plt.plot([target_threshold_charge, target_threshold_charge], [plt.ylim()[0], plt.ylim()[1]], 'b--', linewidth=2, label='Threshold $%d$ e' % target_threshold_charge)
@@ -128,8 +127,8 @@ def plot_landau(source_scan_filename, tdc_hists, target_threshold, fit_range=(13
 
     #   TDC measurements
     plsr_dacs = [target_threshold, 40, 50, 60, 80, 100, 120, 150, 200, 250, 300, 350, 400, 500, 600, 700, 800]  # PlsrDAC range for TDC calibration, should start at threshold
-    col_span = [55, 75]#[50, 78]  # pixel column range to use in TDC scans
-    row_span = [125, 225]#[20, 315]  # pixel row range to use in TDC scans
+    col_span = [55, 75]  # [50, 78]  # pixel column range to use in TDC scans
+    row_span = [125, 225]  # [20, 315]  # pixel row range to use in TDC scans
     tdc_pixel = make_box_pixel_mask_from_col_row(column=[col_span[0], col_span[1]], row=[row_span[0], row_span[1]])  # edge pixel are not used in analysis
 
     runmngr = RunManager('configuration.yaml')
@@ -150,18 +149,18 @@ def plot_landau(source_scan_filename, tdc_hists, target_threshold, fit_range=(13
     runmngr.run_run(run=Fei4Tuning, run_conf={'target_threshold': target_threshold, 'target_tot': target_tot, 'target_charge': target_charge}, catch_exception=False)
     runmngr.run_run(run=AnalogScan, run_conf={'scan_parameters': [('PlsrDAC', target_charge)]})
     runmngr.run_run(run=FastThresholdScan)
-    runmngr.run_run(run=StuckPixelScan)
+    runmngr.run_run(run=StuckPixelTuning)
     runmngr.run_run(run=NoiseOccupancyTuning, run_conf={'occupancy_limit': 1000, 'n_triggers': 10000000})  # high occupancy limit to work with strong Sr-90 source
     runmngr.run_run(run=PlsrDacScan, run_conf={"colpr_address": range(25, 39)})
 
     # TDC calibration
     runmngr.run_run(run=HitOrCalibration, run_conf={
-                                                    'reset_rx_on_error': True,
-                                                    "pixels": (np.dstack(np.where(tdc_pixel == 1))+ 1).tolist()[0],
-                                                    "scan_parameters": [('column', None),
-                                                                        ('row', None),
-                                                                        ('PlsrDAC', plsr_dacs)]
-                                                    })
+        'reset_rx_on_error': True,
+        "pixels": (np.dstack(np.where(tdc_pixel == 1)) + 1).tolist()[0],
+        "scan_parameters": [('column', None),
+                            ('row', None),
+                            ('PlsrDAC', plsr_dacs)]
+    })
     calibration_filename = runmngr.current_run.output_filename + '_calibration.h5'
 
     # Scintillator trigger source scan

examples/example_tuning_script/example_tuning_script.py

@@ -34,7 +34,7 @@
     print 'Status:', status
 
     # masking noisy and hot pixels
-    status = runmngr.run_run(run=StuckPixelScan, run_conf=run_conf)
+    status = runmngr.run_run(run=StuckPixelTuning, run_conf=run_conf)
     print 'Status:', status
 
     status = runmngr.run_run(run=NoiseOccupancyTuning, run_conf=run_conf)