viewer: fix MSVC compatibility in viewer-reachable code

Address portability issues found building jfjoch_viewer with MSVC:

- common/{ADUHistogram,AzimuthalIntegrationProfile}.h and
  image_analysis/spot_finding/StrongPixelSet.h only need DeviceOutput,
  so include fpga/pcie_driver/jfjoch_fpga.h (plain-C, self-contained)
  directly instead of acquisition_device/AcquisitionDevice.h, which
  dragged <unistd.h> into the viewer tree.
- common/time_utc.h: guard gmtime_r/timegm/localtime_r with the MSVC
  equivalents (gmtime_s/_mkgmtime/localtime_s) under _WIN32; drop the
  duplicated includes and add the headers used directly.
- gemmi_gph/gemmi/utf.hpp: vendor the upstream gemmi header; fileutil.hpp
  includes it on Windows for UTF8_to_wchar but it was never vendored.
- writer/HDF5Objects.cpp: ExtractFilename returns path.filename().string()
  (std::filesystem::path has no implicit conversion to std::string on
  Windows, where it is wchar_t-based).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

common/ADUHistogram.h

@@ -5,7 +5,7 @@
 
 #include <mutex>
 #include "MultiLinePlot.h"
-#include "../acquisition_device/AcquisitionDevice.h"
+#include "../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
 
 class ADUHistogram {
     mutable std::mutex m;

common/AzimuthalIntegrationProfile.h

@@ -8,7 +8,7 @@
 #include "MultiLinePlot.h"
 
 #include "AzimuthalIntegrationMapping.h"
-#include "../acquisition_device/AcquisitionDevice.h"
+#include "../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
 
 class AzimuthalIntegrationProfile {
     mutable std::mutex m;

common/time_utc.h

@@ -7,10 +7,10 @@
 #include <chrono>
 #include <regex>
 #include <iomanip>
-#include <string>
-#include <chrono>
-#include <regex>
-#include <iomanip>
+#include <sstream>
+#include <stdexcept>
+#include <ctime>
+#include <cstdio>
 
 inline std::string time_UTC(const std::chrono::time_point<std::chrono::system_clock> &input) {
     auto time_ms = std::chrono::duration_cast<std::chrono::milliseconds>(input.time_since_epoch()).count();
@@ -19,8 +19,12 @@ inline std::string time_UTC(const std::chrono::time_point<std::chrono::system_cl
     time_t time = time_ms / (1000);
 
     std::tm tm_utc{};
+#ifdef _WIN32
+    if (gmtime_s(&tm_utc, &time) != 0)
+#else
     if (gmtime_r(&time, &tm_utc) == nullptr)
-        throw std::runtime_error("gmtime_r failed");
+#endif
+        throw std::runtime_error("gmtime failed");
 
     strftime(buf1, sizeof(buf1), "%FT%T", &tm_utc);
     snprintf(buf2, sizeof(buf2), ".%03ld", time_ms % 1000);
@@ -58,7 +62,11 @@ inline uint64_t parse_UTC_to_ms(const std::string& utc_string) {
         milliseconds = std::stoi(frac);
     }
 
+#ifdef _WIN32
+    time_t t = _mkgmtime(&tm);
+#else
     time_t t = timegm(&tm);
+#endif
     return static_cast<uint64_t>(t) * 1000ULL + milliseconds;
 }
 
@@ -71,7 +79,11 @@ inline std::string utc_to_local_human_readable(const std::string& utc_string) {
         time_t t = system_clock::to_time_t(tp);
 
         std::tm tm_local{};
+#ifdef _WIN32
+        if (localtime_s(&tm_local, &t) != 0)
+#else
         if (localtime_r(&t, &tm_local) == nullptr)
+#endif
             return "";
 
         static const char* months[] = {

gemmi_gph/gemmi/utf.hpp

@@ -0,0 +1,78 @@
+// Copyright 2017 Global Phasing Ltd.
+//
+// Conversion between UTF-8 and wchar. Used only for file names on Windows.
+
+#ifndef GEMMI_UTF_HPP_
+#define GEMMI_UTF_HPP_
+
+#include <string>
+
+namespace gemmi {
+
+// from Mark Ransom's answer
+// https://stackoverflow.com/questions/148403/utf8-to-from-wide-char-conversion-in-stl/148766#148766
+inline std::wstring UTF8_to_wchar(const char* in) {
+  std::wstring out;
+  unsigned int codepoint = 0;
+  while (*in != 0) {
+    unsigned char ch = static_cast<unsigned char>(*in);
+    if (ch <= 0x7f)
+      codepoint = ch;
+    else if (ch <= 0xbf)
+      codepoint = (codepoint << 6) | (ch & 0x3f);
+    else if (ch <= 0xdf)
+      codepoint = ch & 0x1f;
+    else if (ch <= 0xef)
+      codepoint = ch & 0x0f;
+    else
+      codepoint = ch & 0x07;
+    ++in;
+    if ((*in & 0xc0) != 0x80 && codepoint <= 0x10ffff) {
+      if (sizeof(wchar_t) > 2) {
+        out.append(1, static_cast<wchar_t>(codepoint));
+      } else if (codepoint > 0xffff) {
+        out.append(1, static_cast<wchar_t>(0xd800 + (codepoint >> 10)));
+        out.append(1, static_cast<wchar_t>(0xdc00 + (codepoint & 0x03ff)));
+      } else if (codepoint < 0xd800 || codepoint >= 0xe000) {
+        out.append(1, static_cast<wchar_t>(codepoint));
+      }
+    }
+  }
+  return out;
+}
+
+inline std::string wchar_to_UTF8(const wchar_t* in) {
+  std::string out;
+  unsigned int codepoint = 0;
+  while (*in != 0) {
+    if (*in >= 0xd800 && *in <= 0xdbff) {
+      codepoint = ((*in - 0xd800) << 10) + 0x10000;
+    } else {
+      if (*in >= 0xdc00 && *in <= 0xdfff)
+        codepoint |= *in - 0xdc00;
+      else
+        codepoint = *in;
+      if (codepoint <= 0x7f) {
+        out += static_cast<char>(codepoint);
+      } else if (codepoint <= 0x7ff) {
+        out += static_cast<char>(0xc0 | ((codepoint >> 6) & 0x1f));
+        out += static_cast<char>(0x80 | (codepoint & 0x3f));
+      } else if (codepoint <= 0xffff) {
+        out += static_cast<char>(0xe0 | ((codepoint >> 12) & 0x0f));
+        out += static_cast<char>(0x80 | ((codepoint >> 6) & 0x3f));
+        out += static_cast<char>(0x80 | (codepoint & 0x3f));
+      } else {
+        out += static_cast<char>(0xf0 | ((codepoint >> 18) & 0x07));
+        out += static_cast<char>(0x80 | ((codepoint >> 12) & 0x3f));
+        out += static_cast<char>(0x80 | ((codepoint >> 6) & 0x3f));
+        out += static_cast<char>(0x80 | (codepoint & 0x3f));
+      }
+      codepoint = 0;
+    }
+    ++in;
+  }
+  return out;
+}
+
+} // namespace gemmi
+#endif

image_analysis/spot_finding/StrongPixelSet.h

@@ -5,7 +5,7 @@
 
 #include "../../common/DiffractionExperiment.h"
 #include "../../common/DiffractionSpot.h"
-#include "../../acquisition_device/AcquisitionDevice.h"
+#include "../../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
 #include "SpotFindingSettings.h"
 
 struct strong_pixel {

writer/HDF5Objects.cpp

@@ -1014,7 +1014,7 @@ CompressionAlgorithm HDF5Dcpl::GetCompression() {
 std::string ExtractFilename(const std::string& str) {
     std::filesystem::path path(str);
     // if (std::filesystem::is_regular_file(path))
-    return path.filename();
+    return path.filename().string();
 }
 
 bool HDF5Object::GetBool(const std::string &name) const {