From 04146e683ca39d98632e46f2327e9a47228c61eb Mon Sep 17 00:00:00 2001
From: Erik Frojdh <erik.frojdh@gmail.com>
Date: Wed, 10 Apr 2019 16:54:33 +0200
Subject: [PATCH] updated reading

---
 python/scripts/basic.py   | 14 +++++++++++++-
 python/src/Detector.h     |  2 +-
 python/src/main.cpp       |  4 +++-
 python/src/mythenFileIO.h | 20 ++++++++++++++------
 4 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/python/scripts/basic.py b/python/scripts/basic.py
index 1f14422ba..8f199146c 100644
--- a/python/scripts/basic.py
+++ b/python/scripts/basic.py
@@ -1,8 +1,20 @@
 import os
 import sys
+import numpy as np
 sys.path.append(os.path.join(os.getcwd(), 'bin'))
 from sls_detector import Eiger
 from sls_detector import ExperimentalDetector
 
+from _sls_detector.io import read_ctb_file
+
 d = Eiger()
-e = ExperimentalDetector()
\ No newline at end of file
+e = ExperimentalDetector()
+
+# ncols = 192
+# start = 600
+# end = 1800
+# nrows = end-start
+# data = np.zeros((nrows, ncols))
+
+# for i in range(nrows):
+#     data[i, :] = read_ctb_file(f'/home/l_frojdh/mythendata/MoKbZr_30kV60mA_1s_200V_thr{start+i}_1.raw', 8, 24)
\ No newline at end of file
diff --git a/python/src/Detector.h b/python/src/Detector.h
index 52264bbad..39a9db510 100644
--- a/python/src/Detector.h
+++ b/python/src/Detector.h
@@ -19,7 +19,7 @@ class Detector {
     Detector(int i)
         : det(i), multi_detector_id(i) {
         //Disable output from std::cout
-        std::cout.setstate(std::ios_base::failbit);
+        // std::cout.setstate(std::ios_base::failbit);
     }
 
     int getMultiDetectorId() { return multi_detector_id; }
diff --git a/python/src/main.cpp b/python/src/main.cpp
index c338b4328..b7b29bb35 100644
--- a/python/src/main.cpp
+++ b/python/src/main.cpp
@@ -285,7 +285,9 @@ py::class_<multiSlsDetector> multiDetectorApi(m, "multiDetectorApi");
         .def("_setReceiverUDPIP", &multiSlsDetector::setReceiverUDPIP)
             ;
 
-        m.def("hej", &hej, "some");
+    py::module io = m.def_submodule("io", "Submodule for io");
+    io.def("read_ctb_file", &read_ctb_file, "some");
+
 
 #ifdef VERSION_INFO
     m.attr("__version__") = VERSION_INFO;
diff --git a/python/src/mythenFileIO.h b/python/src/mythenFileIO.h
index 0d35ca6c5..c0660c9bc 100644
--- a/python/src/mythenFileIO.h
+++ b/python/src/mythenFileIO.h
@@ -7,6 +7,11 @@
 #include <iostream>
 #include <vector>
 
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+namespace py = pybind11;
+
 template <size_t bit_index0, size_t bit_index1>
 std::vector<int> ExtractBits(const std::vector<uint64_t> &data, int dr = 24) {
     constexpr int mask0 = (1 << bit_index0);
@@ -50,11 +55,11 @@ std::vector<int> ExtractBits(const std::vector<uint64_t> &data, int dr = 24) {
     return result;
 }
 
-std::vector<uint64_t> ReadFile(const std::string &fname, int offset = 8, int dr = 24) {
+std::vector<uint64_t> ReadFile(const std::string &fname, int offset = 8,
+                               int dr = 24) {
     const int element_size = static_cast<int>(sizeof(uint64_t));
     const int byte_offset = element_size * offset;
     const int expected_size = dr * element_size * 32 * 3;
-
     std::ifstream fs(fname, std::ios::binary | std::ios::ate);
     if (!fs.is_open()) {
         throw std::runtime_error("File not found: " + std::string(fname));
@@ -63,15 +68,18 @@ std::vector<uint64_t> ReadFile(const std::string &fname, int offset = 8, int dr
     if (data_size != expected_size) {
         auto diff = data_size - expected_size;
         std::cout << "WARNING: data size is: " << data_size
-                  << " expected size is: " << expected_size << ", " << std::abs(diff) << " bytes "
+                  << " expected size is: " << expected_size << ", "
+                  << std::abs(diff) << " bytes "
                   << ((diff < 0) ? "missing" : "too many") << '\n';
     }
     std::vector<uint64_t> data(expected_size / element_size);
     fs.seekg(byte_offset, std::ios::beg);
-    fs.read(reinterpret_cast<char *>(data.data()), data_size);
+    fs.read(reinterpret_cast<char *>(data.data()), expected_size);
     return data;
 }
 
-int hej(){
-    return 5;
+py::array_t<uint64_t> read_ctb_file(const std::string &fname, int offset = 8,
+                                    int dr = 24) {
+    auto data = ExtractBits<17, 6>(ReadFile(fname, offset, dr));
+    return py::array(data.size(), data.data());
 }