Release APT Calibrator 4.0.4

APT Calibrator 4.0.4 is now available:
https://dasapt.com/forum/download

This version is about editing mass ranges directly on the spectrum, and measuring composition along a cylinder in the 3D reconstruction. If you already have 4.0.3, the software should offer this update at startup.

How to edit RRNG on the mass spectrum

Load a POS / EPOS file so the mass spectrum is shown. Use the RRNG button if you want the range table as well. You can start from an existing .rrng (Load RRNG) or build ranges on the plot.

1. Add a peak. Right-click on a peak: the menu offers Add peak at … Da, and the software estimates a window around that peak. Then type the ion name (for example Fe or Fe++).
2. Add a range by dragging. Hold the right mouse button and drag across the peak (orange box). On release you get the same ion-name dialog, using the exact Da interval you drew. This is better when the automatic window is too wide or too narrow.
3. Adjust bounds. Move the cursor to the left or right coloured edge of a range until it becomes a left–right arrow, then drag. The selected range is drawn stronger. You can also edit numbers in the RRNG table.
4. Delete. Right-click inside an existing range and choose Delete, or select the row in the RRNG table and use Delete.
5. Apply. Changing ranges does not recolour the 3D view until you click Update analysis (it shows a * while there are unapplied edits). Zoom on the spectrum is kept. If you already computed an iso-surface or volume map, recompute those after the new ranges.
6. Save. Save RRNG writes the current file; Export RRNG asks for a new path. Both are also on the right-click menu. The 3D legend checkboxes still hide or show each range without changing the file.

Left-drag on the spectrum zooms; mouse wheel zooms at the cursor; double-click restores the full range.

How to use the cylinder 1D profile

You need reconstructed XYZ (a POS file, or an EPOS that already contains XYZ). Then click Cylinder on the toolbar.

1. A half-transparent solid cylinder appears in the 3D view, and the Cylinder 1D profile window opens. Fit to data places it on the specimen (default axis is Z).
2. Move: drag a red / green / blue arrow to slide along X / Y / Z, or drag the cylinder body to move it freely.
3. Rotate: drag a coloured ring. The axis list switches to Custom when it is no longer aligned with X, Y or Z. You can also pick X, Y or Z (specimen) in the window.
4. Radius: drag the cylinder wall, or type Radius (nm). Length is set in the window (Length, nm) or by Fit to data — the gizmo does not stretch the length.
5. Optional: Clip atoms to cylinder hides atoms outside the ROI in the 3D view. Show cylinder only toggles the overlay.
6. Set Bin width (nm), then click Compute 1D profile. The plot uses the current RRNG colours. Quantity can be concentration (at.%), counts, or density (at/nm³). Distance is along the cylinder axis.
7. If the cylinder is empty, increase radius or length, or Fit to data again. Export CSV writes the profile. Clear removes the ROI.

Composition follows the ranges you applied with Update analysis, so edit RRNG first if the ion colours should change.

中文使用说明

APT Calibrator 4.0.4 下载：https://dasapt.com/forum/download
已安装 4.0.3 时，启动一般会提示更新。

质谱上改 RRNG

先打开 POS / EPOS，显示出质谱。需要表格时点工具栏 RRNG。可以 Load 已有 .rrng，也可以直接在图上画峰。

1. 加点峰：在峰上右键，选 Add peak at … Da。程序会按峰形估一个窗口，然后输入离子名（如 Fe、Fe++）。
2. 拖出质量范围：按住右键在峰上拖（橙色框）。松开后同样问离子名，范围就是你画出的 Da 区间。自动窗口不准时用这个更合适。
3. 改边界：把鼠标放到彩色范围的左或右边缘，指针变成左右箭头后再拖。当前选中的范围会画得更明显。也可以在 RRNG 表里改数字。
4. 删除：在已有范围内右键选 Delete，或在表中选中一行再 Delete。
5. 生效：改范围不会立刻重画三维，需要点 Update analysis（有未应用修改时按钮带 *）。质谱缩放会保留。如果已经算过等值面或体素图，改完范围后请重新计算。
6. 保存：Save RRNG 写回当前文件，Export RRNG 另存。右键菜单里也有这两项。三维图例前的勾选只控制显示，不会改文件。

质谱上左键拖是缩放，滚轮在光标处缩放，双击恢复全谱。

圆柱一维成分剖面

需要已有重构坐标（POS，或带 XYZ 的 EPOS）。点工具栏 Cylinder。

1. 三维里出现半透明实心圆柱，并打开 Cylinder 1D profile 窗口。Fit to data 会按试样放好圆柱（默认沿 Z）。
2. 平移：拖红 / 绿 / 蓝箭头沿 X / Y / Z 移动，或直接拖圆柱体自由平移。
3. 旋转：拖彩色圆环。轴不再沿 X/Y/Z 时，列表会变成 Custom。也可以在窗口里选 X、Y 或 Z（试样方向）。
4. 半径：拖圆柱壁，或改 Radius (nm)。长度请在窗口里改 Length (nm)，或用 Fit to data。三维操纵器不能拉长圆柱。
5. 可选：Clip atoms to cylinder 只显示圆柱内的原子；Show cylinder 只开关圆柱显示。
6. 设好 Bin width (nm)，再点 Compute 1D profile。曲线颜色跟当前 RRNG 一致。Quantity 可选浓度 (at.%)、计数或密度 (at/nm³)。横轴是沿圆柱轴向的距离。
7. 如果提示圆柱是空的，加大半径或长度，或再 Fit to data。Export CSV 导出剖面，Clear 去掉 ROI。

成分统计用的是你点过 Update analysis 之后的质量范围，所以若要改离子着色，请先改 RRNG 再计算剖面。